U.S. patent application number 12/083824 was filed with the patent office on 2012-06-21 for method and device for the in vitro analysis for mrna of genes involved in haematological neoplasias.
Invention is credited to Patricia Alvarez Cabeza, Pilar Giraldo Castellano, Miguel Pocovi Mieras.
Application Number | 20120157329 12/083824 |
Document ID | / |
Family ID | 37967431 |
Filed Date | 2012-06-21 |
United States Patent
Application |
20120157329 |
Kind Code |
A1 |
Giraldo Castellano; Pilar ;
et al. |
June 21, 2012 |
Method and Device for the in Vitro Analysis for MRNA of Genes
Involved in Haematological Neoplasias
Abstract
Method and device for the in vitro analysis of mRNA of genes
involved in hematological neoplasias. The device, composed of
probes which specifically hybridize with genes involved in
hematological neoplasias, designed so that its behaviour in the
hybridization is similar, permits the evaluation of the mRNA level
in biological samples taken from subjects suspected to be suffering
from hematological neoplasia and facilitating the comparison
between the different samples and their grouping by similarity in
the gene expression patterns, especially when the probes are
disposed in the form of microarray. The application of the method
of the invention to obtain and process data of gene expression
differences from the device of the invention permits the
identification of genes significant for distinguishing samples
associated to hematological neoplasias, facilitates the diagnosis
of neoplasias as CLL and permits making a prognosis of the
evolution thereof.
Inventors: |
Giraldo Castellano; Pilar;
(Zaragoza, ES) ; Alvarez Cabeza; Patricia;
(Zaragoza, ES) ; Pocovi Mieras; Miguel; (Zaragoza,
ES) |
Family ID: |
37967431 |
Appl. No.: |
12/083824 |
Filed: |
May 8, 2006 |
PCT Filed: |
May 8, 2006 |
PCT NO: |
PCT/ES2006/070054 |
371 Date: |
October 2, 2009 |
Current U.S.
Class: |
506/9 ; 435/6.11;
506/16; 536/24.3; 702/19 |
Current CPC
Class: |
C12Q 1/6886 20130101;
C12Q 2600/112 20130101; C12Q 2600/158 20130101; C12Q 2600/118
20130101 |
Class at
Publication: |
506/9 ; 435/6.11;
506/16; 536/24.3; 702/19 |
International
Class: |
C40B 30/04 20060101
C40B030/04; G06F 19/24 20110101 G06F019/24; C07H 21/00 20060101
C07H021/00; C12Q 1/68 20060101 C12Q001/68; C40B 40/06 20060101
C40B040/06 |
Foreign Application Data
Date |
Code |
Application Number |
Oct 27, 2005 |
ES |
200502618 |
Claims
1. A composition which comprises at least one oligonucleotide from
the group composed of: SG1, SG2, SG3, SG4, SG5, SG6, SG7, SG8, SG9,
SG10, SG11, SG12, SG13, SG14, SG15, SG16, SG17, SG18, SG19, SG20,
SG21, SG22, SG23, SG24, SG25, SG26, SG27, SG28, SG29, SG30, SG31,
SG32, SG33, SG34, SG35, SG36, SG37, SG38, SG39, SG40, SG41, SG42,
SG43, SG44, SG45, SG46, SG47, SG48, SG49, SG50, SG51, SG52, SG53,
SG54, SG55, SG56, SG57, SG58, SG59, SG60, SG61, SG62, SG63, SG64,
SG65, SG66, SG67, SG68, SG69, SG70, SG71, SG72, SG73, SG74, SG75,
SG76, SG77, SG78, SG79, SG80, SG81, SG82, SG83, SG84, SG85, SG86,
SG87, SG88, SG89, SG90, SG91, SG92, SG93, SG94, SG95, SG96, SG97,
SG98, SG99, SG100, SG101, SG102, SG103, SG104, SG105, SG106, SG107,
SG108, SG109, SG110, SG111, SG112, SG113, SG114, SG115, SG116,
SG117, SG118, SG119, SG120, SG121, SG122, SG123, SG124, SG125,
SG126, SG127, SG128, SG129, SG130, SG131, SG132, SG133, SG134,
SG135, SG136, SG137, SG138, SG139, SG140, SG141, SG142, SG143,
SG144, SG145, SG146, SG147, SG148, SG149, SG150, SG151, SG152,
SG153, SG154, SG155, SG156, SG157, SG158, SG159, SG160, SG161,
SG162, SG163, SG164, SG165, SG166, SG167, SG168, SG169, SG170,
SG171, SG172, SG173, SG174, SG175, SG176, SG177, SG178, SG179,
SG180, SG181, SG182, SG183, SG184, SG185, SG186, SG187, SG188,
SG189, SG190, SG191, SG192, SG193, SG194, SG195, SG196, SG197,
SG198, SG199, SG200, SG201, SG202, SG203, SG204, SG205, SG206,
SG207, SG208, SG209, SG210, SG211, SG212, SG213, SG214, SG215,
SG216, SG217, SG218, SG219, SG220, SG221, SG222, SG223, SG224,
SG225, SG226, SG227, SG228, SG229, SG230, SG231, SG232, SG233,
SG234, SG235, SG236, SG237, SG238, SG239, SG240, SG241, SG242,
SG243, SG244, SG245, SG246, SG247, SG248, SG249, SG250, SG251,
SG252, SG253, SG254, SG255, SG256, SG257, SG258, SG259, SG260,
SG261, SG262, SG263, SG264, SG265, SG266, SG267, SG268, SG269,
SG270, SG271, SG272, SG273, SG274, SG275, SG276, SG277, SG278,
SG279, SG280, SG281, SG282, SG283, SG284, SG285, SG286, SG287,
SG288, SG289, SG290, SG291, SG292, SG293, SG294, SG295, SG296,
SG297, SG298, SG299, SG300, SG301, SG302, SG303, SG304, SG305,
SG306, SG307, SG308, SG309, SG310, SG311, SG312, SG313, SG314,
SG315, SG316, SG317, SG318, SG319, SG320, SG321, SG322, SG323,
SG324, SG325, SG326, SG327, SG328, SG329, SG330, SG331, SG332,
SG333, SG334, SG335, SG336, SG337, SG338, SG339, SG340, SG341,
SG342, SG343, SG344, SG345, SG346, SG347, SG348, SG349, SG350,
SG351, SG352, SG353, SG354, SG355, SG356, SG357, SG358, SG359,
SG360, SG361, SG362, SG363, SG364, SG365, SG366, SG367, SG368,
SG369, SG370, SG371, SG372, SG373, SG374, SG375, SG376, SG377,
SG378, SG379, SG380, SG381, SG382, SG383, SG384, SG385, SG386,
SG387, SG388, SG389, SG390, SG391, SG392, SG393, SG394, SG395,
SG396, SG397, SG398, SG399, SG400, SG401, SG402, SG403, SG404,
SG405, SG406, SG407, SG408, SG409, SG410, SG411, SG412, SG413,
SG414, SG415, SG416, SG417, SG418, SG419, SG420, SG421, SG422,
SG423, SG424, SG425, SG426, SG427, SG428, SG429, SG430, SG431,
SG432, SG433, SG434, SG435, SG436, SG437, SG438, SG439, SG440,
SG441, SG442, SG443, SG444, SG445, SG446, SG447, SG448, SG449,
SG450, SG451, SG452, SG453, SG454, SG455, SG456, SG457, SG458,
SG459, SG460, SG461, SG462, SG465, SG468, SG469, SG470, SG471,
SG472, SG473, SG474, SG475, SG476, SG477, SG478, SG479, SG480,
SG481, SG482, SG483, SG484, SG485, SG486, SG487, SG488, SG489,
SG490, SG491, SG492, SG493, SG494, SG495, SG496, SG497, SG498,
SG499, SG500, SG501, SG502, SG503, SG504, SG505, SG506, SG507,
SG508, SG509, SG510, SG511, SG512, SG513, SG514, SG515, SG516,
SG517, SG518, SG519, SG520, SG521, SG522, SG523, SG524, SG525,
SG526, SG527, SG428, SG529, SG530, SG531, SG532, SG533, SG534,
SG535, SG536, SG537, SG538, SG539, SG540, SG541, SG542, SG543,
SG544, SG545, SG546, SG547, SG548, SG549, SG550, SG551, SG552,
SG553, SG554, SG555, SG556, SG557, SG558, SG559, SG560, SG561,
SG562, SG563, or combinations thereof, to be used as probe in the
determination of the expression level of a gene which possesses a
sequence complementary to said oligonucleotide by the evaluation of
the mRNA level corresponding to that gene, of application in the in
vitro diagnosis of neoplasias originating from hematopoietic cells
and/or in the in vitro prognosis of the evolution of said
disease.
2. A composition according to claim 1, which comprises at least the
oligonucleotides SG117, SG428, SG459, SG507, SG508.
3. A composition according to claim 2, which additionally comprises
at least oligonucleotides SG461 and SG493.
4. A composition according to claim 2, which additionally comprises
at least the oligonucleotide SG237.
5. A composition according to claim 4, which additionally comprises
at least one oligonucleotide selected from the group of SG2, SG4,
SG8, SG10, SG13, SG15, SG16, SG19, SG20, SG23, SG26, SG28, SG31,
SG34, SG36, SG39, SG48, SG58, SG60, SG65, SG76, SG77, SG84, SG89,
SG94, SG9, SG97, SG99, SG102, SG106, SG107, SG463, SG115, SG116,
SG120, SG129, SG134, SG135, SG138, SG139, SG141, SG145, SG158,
SG161, SG163, SG176, SG178, SG185, SG207, SG208, SG210, SG217,
SG227, SG231, SG237, SG264, SG272, SG277, SG281, SG283, SG286,
SG294, SG298, SG299, SG307, SG308, SG319, SG328, SG330, SG333,
SG336, SG342, SG344, SG345, SG347, SG361, SG384, SG389, SG395,
SG404, SG407, SG416, SG423, SG430, SG432, SG434, SG444, SG446,
SG453, SG458, SG464, SG465, SG466, SG467, SG471, SG473, SG474,
SG475, SG481, SG485, SG487, SG491, SG498, SG511, SG517, SG518,
SG522, SG526, SG530, SG533, SG538, SG541, SG554, SG558, SG561 or
combinations thereof.
6. A composition according to claim 2, to be used in the in vitro
diagnosis of chronic lymphatic leukemia.
7. A composition according to claim 1, which comprises at least
oligonucleotides SG26, SG216, SG366.
8. A composition according to claim 7, which additionally comprises
at least one oligonucleotide selected from the group of SG31,
SG177, SG194, SG195, SG197, SG213, SG293, SG301, SG309, SG333,
SG343, SG357, SG439, SG452, SG555, SG556.
9. A composition according to claim 7, to be used in the in vitro
prognosis of the future evolution of the disease in a patient
suffering from chronic lymphatic leukemia.
10. A composition according to claim 1, which comprises the
totality of the nucleotides of the group composed of: SG1, SG2,
SG3, SG4, SG5, SG6, SG7, SG8, SG9, SG10, SG11, SG12, SG13, SG14,
SG15, SG16, SG17, SG18, SG19, SG20, SG21, SG22, SG23, SG24, SG25,
SG26, SG27, SG28, SG29, SG30, SG31, SG32, SG33, SG34, SG35, SG36,
SG37, SG38, SG39, SG40, SG41, SG42, SG43, SG44, SG45, SG46, SG47,
SG48, SG49, SG50, SG51, SG52, SG53, SG54, SG55, SG56, SG57, SG58,
SG59, SG60, SG61, SG62, SG63, SG64, SG65, SG66, SG67, SG68, SG69,
SG70, SG71, SG72, SG73, SG74, SG75, SG76, SG77, SG78, SG79, SG80,
SG81, SG82, SG83, SG84, SG85, SG86, SG87, SG88, SG89, SG90, SG91,
SG92, SG93, SG94, SG95, SG96, SG97, SG98, SG99, SG100, SG101,
SG102, SG103, SG104, SG105, SG106, SG107, SG108, SG109, SG110,
SG111, SG112, SG113, SG114, SG115, SG116, SG117, SG118, SG119,
SG120, SG121, SG122, SG123, SG124, SG125, SG126, SG127, SG128,
SG129, SG130, SG131, SG132, SG133, SG134, SG135, SG136, SG137,
SG138, SG139, SG140, SG141, SG142, SG143, SG144, SG145, SG146,
SG147, SG148, SG149, SG150, SG151, SG152, SG153, SG154, SG155,
SG156, SG157, SG158, SG159, SG160, SG161, SG162, SG163, SG164,
SG165, SG166, SG167, SG168, SG169, SG170, SG171, SG172, SG173,
SG174, SG175, SG176, SG177, SG178, SG179, SG180, SG181, SG182,
SG183, SG184, SG185, SG186, SG187, SG188, SG189, SG190, SG191,
SG192, SG193, SG194, SG195, SG196, SG197, SG198, SG199, SG200,
SG201, SG202, SG203, SG204, SG205, SG206, SG207, SG208, SG209,
SG210, SG211, SG212, SG213, SG214, SG215, SG216, SG217, SG218,
SG219, SG220, SG221, SG222, SG223, SG224, SG225, SG226, SG227,
SG228, SG229, SG230, SG231, SG232, SG233, SG234, SG235, SG236,
SG237, SG238, SG239, SG240, SG241, SG242, SG243, SG244, SG245,
SG246, SG247, SG248, SG249, SG250, SG251, SG252, SG253, SG254,
SG255, SG256, SG257, SG258, SG259, SG260, SG261, SG262, SG263,
SG264, SG265, SG266, SG267, SG268, SG269, SG270, SG271, SG272,
SG273, SG274, SG275, SG276, SG277, SG278, SG279, SG280, SG281,
SG282, SG283, SG284, SG285, SG286, SG287, SG288, SG289, SG290,
SG291, SG292, SG293, SG294, SG295, SG296, SG297, SG298, SG299,
SG300, SG301, SG302, SG303, SG304, SG305, SG306, SG307, SG308,
SG309, SG310, SG311, SG312, SG313, SG314, SG315, SG316, SG317,
SG318, SG319, SG320, SG321, SG322, SG323, SG324, SG325, SG326,
SG327, SG328, SG329, SG330, SG331, SG332, SG333, SG334, SG335,
SG336, SG337, SG338, SG339, SG340, SG341, SG342, SG343, SG344,
SG345, SG346, SG347, SG348, SG349, SG350, SG351, SG352, SG353,
SG354, SG355, SG356, SG357, SG358, SG359, SG360, SG361, SG362,
SG363, SG364, SG365, SG366, SG367, SG368, SG369, SG370, SG371,
SG372, SG373, SG374, SG375, SG376, SG377, SG378, SG379, SG380,
SG381, SG382, SG383, SG384, SG385, SG386, SG387, SG388, SG389,
SG390, SG391, SG392, SG393, SG394, SG395, SG396, SG397, SG398,
SG399, SG400, SG401, SG402, SG403, SG404, SG405, SG406, SG407,
SG408, SG409, SG410, SG411, SG412, SG413, SG414, SG415, SG416,
SG417, SG418, SG419, SG420, SG421, SG422, SG423, SG424, SG425,
SG426, SG427, SG428, SG429, SG430, SG431, SG432, SG433, SG434,
SG435, SG436, SG437, SG438; SG439, SG440, SG441, SG442, SG443,
SG444, SG445, SG446, SG447, SG448, SG449, SG450, SG451, SG452,
SG453, SG454, SG455, SG456, SG457, SG458, SG459, SG460, SG461,
SG462, SG465, SG468, SG469, SG470, SG471, SG472, SG473, SG474,
SG475, SG476, SG477, SG478, SG479, SG480, SG481, SG482, SG483,
SG484, SG485, SG486, SG487, SG488, SG489, SG490, SG491, SG492,
SG493, SG494, SG495, SG496, SG497, SG498, SG499, SG500, SG501,
SG502, SG503, SG504, SG505, SG506, SG507, SG508, SG509, SG510,
SG511, SG512, SG513, SG514, SG515, SG516, SG517, SG518, SG519,
SG520, SG521, SG522, SG523, SG524, SG525, SG526, SG527, SG428,
SG529, SG530, SG531, SG532, SG533, SG534, SG535, SG536, SG537,
SG538, SG539, SG540, SG541, SG542, SG543, SG544, SG545, SG546,
SG547, SG548, SG549, SG550, SG551, SG552, SG553, SG554, SG555,
SG556, SG557, SG558, SG559, SG560, SG561, SG562, SG563.
11. A composition according to claim 1, characterized in that it
additionally comprises at least one oligonucleotide selected from
the group composed of SG463, SG464, SG466, SG467, SSPC1, SSPC2,
SSPC3, SSPC4, SSPC5, SSPC6, SSPC7, SCN1, SCN2, SCN3, SCN5, SCN6,
SCN7, SCN8, SCN10, SCN11, SCN12, SCN13, SC1, SC2, SC3, SC4, SC5,
SC6 and SC7.
12. A composition according to claim 11, which comprises all the
oligonucleotides from the group composed of SG463, SG464, SG466,
SG467, SSPC1, SSPC2, SSPC3, SSPC4, SSPC5, SSPC6, SSPC7, SCN1, SCN2,
SCN3, SCN5, SCN6, SCN7, SCN8, SCN10, SCN11, SCN12, SCN13, SC1, SC2,
SC3, SC4, SC5, SC6 and SC7.
13. A composition according to claim 1, wherein the
oligonucleotides are disposed on a solid support.
14. A composition according to claim 13, wherein the
oligonucleotides are disposed in an ordered fashion on a solid
support which is glass similar to a slide whereto the
oligonucleotides are bound by covalent bonds, forming a
microarray.
15. A composition in the form of microarray according to claim 14,
which comprises the totality of the oligonucleotides from the group
composed of SG1, SG2, SG3, SG4, SG5, SG6, SG7, SG8, SG9, SG10,
SG11, SG12, SG13, SG14, SG15, SG16, SG17, SG18, SG19, SG20, SG21,
SG22, SG23, SG24, SG25, SG26, SG27, SG28, SG29, SG30, SG31, SG32,
SG33, SG34, SG35, SG36, SG37, SG38, SG39, SG40, SG41, SG42, SG43,
SG44, SG45, SG46, SG47, SG48, SG49, SG50, SG51, SG52, SG53, SG54,
SG55, SG56, SG57, SG58, SG59, SG60, SG61, SG62, SG63, SG64, SG65,
SG66, SG67, SG68, SG69, SG70, SG71, SG72, SG73, SG74, SG75, SG76,
SG77, SG78, SG79, SG80, SG81, SG82, SG83, SG84, SG85, SG86, SG87,
SG88, SG89, SG90, SG91, SG92, SG93, SG94, SG95, SG96, SG97, SG98,
SG99, SG100, SG101, SG102, SG103, SG104, SG105, SG106, SG107,
SG108, SG109, SG110, SG111, SG112, SG113, SG114, SG115, SG116,
SG117, SG118, SG119, SG120, SG121, SG122, SG123, SG124, SG125,
SG126, SG127, SG128, SG129, SG130, SG131, SG132, SG133, SG134,
SG135, SG136, SG137, SG138, SG139, SG140, SG141, SG142, SG143,
SG144, SG145, SG146, SG147, SG148, SG149, SG150, SG151, SG152,
SG153, SG154, SG155, SG156, SG157, SG158, SG159, SG160, SG161,
SG162, SG163, SG164, SG165, SG166, SG167, SG168, SG169, SG170,
SG171, SG172, SG173, SG174, SG175, SG176, SG177, SG178, SG179,
SG180, SG181, SG182, SG183, SG184, SG185, SG186, SG187, SG188,
SG189, SG190, SG191, SG192, SG193, SG194, SG195, SG196, SG197,
SG198, SG199, SG200, SG201, SG202, SG203, SG204, SG205, SG206,
SG207, SG208, SG209, SG210, SG211, SG212, SG213, SG214, SG215,
SG216, SG217, SG218, SG219, SG220, SG221, SG222, SG223, SG224,
SG225, SG226, SG227, SG228, SG229, SG230, SG231, SG232, SG233,
SG234, SG235, SG236, SG237, SG238, SG239, SG240, SG241, SG242,
SG243, SG244, SG245, SG246, SG247, SG248, SG249, SG250, SG251,
SG252, SG253, SG254, SG255, SG256, SG257, SG258, SG259, SG260,
SG261, SG262, SG263, SG264, SG265, SG266, SG267, SG268, SG269,
SG270, SG271, SG272, SG273, SG274, SG275, SG276, SG277, SG278,
SG279, SG280, SG281, SG282, SG283, SG284, SG285, SG286, SG287,
SG288, SG289, SG290, SG291, SG292, SG293, SG294, SG295, SG296,
SG297, SG298, SG299, SG300, SG301, SG302, SG303, SG304, SG305,
SG306, SG307, SG308, SG309, SG310, SG311, SG312, SG313, SG314,
SG315, SG316, SG317, SG318, SG319, SG320, SG321, SG322, SG323,
SG324, SG325, SG326, SG327, SG328, SG329, SG330, SG331, SG332,
SG333, SG334, SG335, SG336, SG337, SG338, SG339, SG340, SG341,
SG342, SG343, SG344, SG345, SG346, SG347, SG348, SG349, SG350,
SG351, SG352, SG353, SG354, SG355, SG356, SG357, SG358, SG359,
SG360, SG361, SG362, SG363, SG364, SG365, SG366, SG367, SG368,
SG369, SG370, SG371, SG372, SG373, SG374, SG375, SG376, SG377,
SG378, SG379, SG380, SG381, SG382, SG383, SG384, SG385, SG386,
SG387, SG388, SG389, SG390, SG391, SG392, SG393, SG394, SG395,
SG396, SG397, SG398, SG399, SG400, SG401, SG402, SG403, SG404,
SG405, SG406, SG407, SG408, SG409, SG410, SG411, SG412, SG413,
SG414, SG415, SG416, SG417, SG418, SG419, SG420, SG421, SG422,
SG423, SG424, SG425, SG426, SG427, SG428, SG429, SG430, SG431,
SG432, SG433, SG434, SG435, SG436, SG437, SG438, SG439, SG440,
SG441, SG442, SG443, SG444, SG445, SG446, SG447, SG448, SG449,
SG450, SG451, SG452, SG453, SG454, SG455, SG456, SG457, SG458,
SG459, SG460, SG461, SG462, SG465, SG468, SG469, SG470, SG471,
SG472, SG473, SG474, SG475, SG476, SG477, SG478, SG479, SG480,
SG481, SG482, SG483, SG484, SG485, SG486, SG487, SG488, SG489,
SG490, SG491, SG492, SG493, SG494, SG495, SG496, SG497, SG498,
SG499, SG500, SG501, SG502, SG503, SG504, SG505, SG506, SG507,
SG508, SG509, SG510, SG511, SG512, SG513, SG514, SG515, SG516,
SG517, SG518, SG519, SG520, SG521, SG522, SG523, SG524, SG525,
SG526, SG527, SG428, SG529, SG530, SG531, SG532, SG533, SG534,
SG535, SG536, SG537, SG538, SG539, SG540, SG541, SG542, SG543,
SG544, SG545, SG546, SG547, SG548, SG549, SG550, SG551, SG552,
SG553, SG554, SG555, SG556, SG557, SG558, SG559, SG560, SG561,
SG562, SG563.
16. A composition in the form of microarray according to claim 15,
which additionally comprises at least one pair of oligonucleotides
selected from that composed of the oligonucleotides SG463 and SG464
and that composed of the oligonucleotides SG466 and SG467, at least
one oligonucleotide from the group composed of SSPC1, SSPC2, SSPC3,
SSPC4, SSPC5, SSPC6 and SSPC7, at least one oligonucleotide from
the group composed of SCN2, SCN3, SCN6, SCN8, SCN11, SCN12 and
SCN13 and at least one oligonucleotide from the group composed of
SC1, SC2, SC3, SC4, SC5, SC6, SC7, SCN1, SCN5, SCN7 and SCN10.
17. A composition in the form of microarray according to claim 16,
which comprises the totality of the oligonucleotides from the group
composed of SG463, SG464, SG466, SG467, SSPC1, SSPC2, SSPC3, SSPC4,
SSPC5, SSPC6, SSPC7, SCN2, SCN3, SCN6, SCN8, SCN11, SCN12, SCN13,
SC1, SC2, SC3, SC4, SC5, SC6, SC7, SCN1, SCN5, SCN7 and SCN10.
18. A composition in the form of microarray according to claim 17,
which additionally comprises points lacking oligonucleotides
wherein the solvent wherein the oligonucleotides are found on being
deposited on said glass is bound to the glass.
19. A composition in the form of microarray according to claim 18,
which comprises at least twelve copies of each one of the different
oligonucleotides present therein, as well as at least twelve points
lacking oligonucleotides wherein the solvent wherein the
oligonucleotides are found on being deposited on said glass is
bound to the glass.
20. A composition in the form of microarray according to claim 18,
wherein in the points lacking oligonucleotides the DMSO solvent is
bound to the glass.
21. A composition in the form of microarray according to claim 15
to be used in the in vitro diagnosis of chronic lymphatic leukemia
and/or for the in vitro prognosis of the evolution of said
disease.
22. A device for the in vitro diagnosis of a neoplasia originating
from hematopoietic cells and/or for the in vitro prognosis of the
evolution thereof, which comprises a composition according to claim
1.
23. A combination comprising the device for the diagnosis of a
neoplasia originating from hematopoietic cells and/or for the in
vitro prognosis of the evolution thereof according to claim 22, and
a composition in the form of microarray wherein the
oligonucleotides are disposed in an ordered fashion on a solid
support which is glass similar to a slide whereto the
oligonucleotides are bound by covalent bonds, forming a
microarray.
24. A combination comprising the device for the in vitro diagnosis
of a neoplasia originating from hematopoietic cells and/or for the
in vitro prognosis of the evolution thereof according to claim 22,
and a composition in the form of microarray.
25. A device for the in vitro diagnosis of a neoplasia originating
from hematopoietic cells and/or for the in vitro prognosis of the
evolution thereof according to claim 23, wherein the neoplasia
which is diagnosed or a whose evolution a prognosis is made of is
chronic lymphatic leukemia.
26. A method for the in vitro diagnosis of a neoplasia originating
from hematopoietic cells and/or in vitro prognosis of the evolution
thereof which comprises the in vitro detection from a biological
sample and the statistical analysis of the expression level of at
least one significant gene for classifying the sample associated or
not to said neoplasia, a gene which is selected from the group
composed of GABARAP, NPM3, ABCB1, ABCB4, ABCC3, ABCC5, ABCC6,
ABHD1, ABL1, ACTN1, AF1q, AKR1A1, ALDH1A1, ALK, ANK2, ANPEP, ANXA6,
ANXA7, APAF1, APEX, ARHGEF2, ARS2, ASNS, ATIC, ATM, ATP50, BAX,
BCL10, BCL2, BCL2A1, BCL2L1, BCL2LAA, BCL3, BCL6, BCL7A, BCL7b,
BCR, BECN1, BIK, BIRC3, BIRC5, BLMH, BLR1, BLVRB, BMI1, BMP6,
BRMS1, BST2, BTG1, BUB1, C21orf33, C5orfl3, CA12, CALD1, CANP2,
CASC3, CASP1, CASP3, CASP4, CASP5, CASP6, CASP7, CASP8, CASP9,
CAST, CATSD, CBFA2T1, CBFB, CCNA1, CCNB1, CCND1, CCND2, CCND3,
CCNE1, CCR6, CCR7, CCT6A, CD14, CD19, CD2, CD22, CD24, CD28, CD33,
CD34, CD36, CD38, CD3E, CD4, CD44, CD47, CD48, CD5, CD58, CD59,
CD6, CD7, CD79A, CD79B, CD8, CD81, CD83, CD86, CD9, CDA, CDC25A,
CDC25B, CDK2, CDK4, CDK5R1, CDKN1A, CDKN1B, CDKN1C, CDKN2A, CDKN2B,
CDKN2C, CDKN3, CDW52, CEBPA, CEBPB, CEBPD, CFL1, CKMT1, CKS2,
CML66, COL3A1, COL4A6, CR2, CREB1, CREBBP, CRYAB, CSF2, CSF3,
CSRP2, CTGF, CTSB, CUZD1, CXADR, CXCL9, CXCR3, CXCR4, CYC1, CYP1A1,
CYP2A6, DAD-1, DAPK1, DCK, DDX6, DEK, DHFR, DLAD, DNAJA1, DNMT3B,
DNTT, DOK1, DPF2, DPP4, DRG1, DRP2, E2F1, EB-1, EBI2, EDF1, EEF1A1,
EEF1B2, EEF1D, EEF1G, EFNB1, EGFR, EGR1, EIF2B2, EIF3S2, EIF4B,
EIF4E, EIF5A, ELF1, ELF4, ENPP1, EphA3, EPOR, ERBB2, ERBB4, ERCC1,
ERCC2, ERCC3, ERCC5, ERCC6, ETS1, ETS2, ETV6, ETV7, EZH2, FABP5,
FADD, FAIM3, FAM38A, FARP1, FAT, FCER2, FCGR3A, FCGR3B, FGFR1,
FGFR3, FGR, FHIT, FKBP9, FLI1, FLJ22169, FLT3, FN1, FNTB, FOS, FUS,
G1P2, GABPB2, GATA1, GATA2, GATA3, GCET2, GDI2, GGA3, GJA1, GLUD1,
GNL3, GOT1, GRB2, GRIA3, GRK4, GSTP1, GSTT1, GUSB, GZMA, H2AFX,
H3F.sub.3A, HCK, HELLS, HIF1A, HIST1H.sub.2BN, HLA-A, HLA-DPA1,
HLA-DQA1, HLA-DRA, HLA-DRB3, HLF, HMMR, HNRPH3, HNRPL, HOXA10,
HOXA9, HOXD8, HOXD9, HRAS, HSD17B1, HSPB1, IBSP, ICAM1, ICAM3, ID2,
IER3, IFRD1, IGFBP2, IGFBP3, IGFIR, IGLV6-57, IL10, IL15, IL1B,
IL2, IL2RA, IL3, IL32, IL3RA, IL4R, IL6, IL6R, IL8, ILF2, IRF1,
IRF2, IRF4, IRF8, ITGA2, ITGA3, ITGA4, ITGA5, ITGA6, ITGAL, ITGAM,
ITGAX, ITGB1, ITGB2, JAK1, JAK2, JUNB, KAI1, KIAA0247, KIAA0864,
KIT, KLF1, KLF13, KRAS2, KRT18, LADH, LAG3, LASP1, LCK, LCP1, LEPR,
LGALS3, LGALS7, LIF, LIMS1, LMO2, LOC285148, LRP, LSP1, LYL1, LYN,
LYZ, MAFB, MAFK, MAGEA1, MAL, MAP3K12, MAP4K1, MAPK10, MAZ, MBP1,
MCL1, MCM3, MCM7, MDM2, MEIS1, MEN1, MERTK, MKI67, MLF1, MLF2, MLL,
MLLT10, MME, MMP2, MMP7, MMP8, MMP9, MNDA, MPL, MPO, MRPL37, MS4A1,
MTCP1, MUC-1, MX1, MYB, MYBL1, MYC, MYOD1, NCALD, NCAM1, NCL,
NDP52, NDRG1, NDUFA1, NDUFB, NF1, NFATC1, NFIC, NFKB1, NFKB1A,
NINJ1, NPM1, NR3C1, NUMA1, NXF1, ODC1, OGGI, OLIG2, OPRD1, p14ARF,
P55CDC, PABPC1, PAX5, PAX6, PAX8, PBX1, PBX3, PCA1, PCD, PCNA,
PDCD1, PDGFA, PDGFRB, PDHA1, PGF, PGRMC1, PICALM, PLA2G6, PLAU,
PLK1, PLP, PLS3, PLZF, PML, PMM1, POLR2c, POU2F2, PPP1CC, PRAME,
PRKCl, PRKCQ, PRKDC, PRL, PRTN3, PSMA5, PSMB4, PSMC5, PSMD7, PTEN,
PTGS1, PTHLH, PTK2, PTK2B, PTN, PTPRCCD, PYGB, RAD51, RAF1, RAG1,
RARA, RARB, RB1, RBBP4, RBBP6, RBBP8, RBP4, RET, RGS1, RGS1, RIS1,
RORA, RPL17, RPL23A, RPL24, RPL36A, RPL37A, RPL41, RPS3, RPS5,
RPS9, RUNX1, RxRA, S100A2, S100A8, SDC1, SDHD, SELE, SELL, SEPW1,
SERPINA9, SERPINB5, SERPNINA9, SFTPB, SIAT4A, SLC7A5, SNRPB,
SOSTDC1, SP1, SPI1, SPN, SPRR1A, SREBF1, SSBP1, STAT1, STAT3,
STAT5B, SUMO1, TACSTD2, TAGLN2, TAL1, TBP, TCEB1, TCF1, TCF3, TCF7,
TCL1A, TCRbeta, TEGT, TERF1, TERT, TFCP2, TFRC, THBS1, THPO, TIA-2,
TIAM1, TK1, TLX1, TMEM4, TNF, TNFRSF10C, TNFRSF1A, TNFRSF25,
TNFRSF5, TNFRSF6, TNFRSF8, TNFSF10, TNFSF5, TNFSF6, TOP2A, TOPORS,
TP73, TRA@, TRADD, TRAF3, TRAP1, TRIB2, TXNRD1, UBE2C, UHRF1,
UVRAG, VCAM1, VEGF, VPREB1, WBSCR20C, WNT16, WT1, XBP1, XPO6,
XRCC3, XRCC5, ZAP70, ZFPL1, ZNF42, ZNFN1A1, ZYX, 18S rRNA, 28S rRNA
and whose expression level is determined by the evaluation of the
concentration of its corresponding mRNA by the use of at least one
probe which has a sequence complementary to a fragment of a strand
of said gene, a probe which is selected from the group of
oligonucleotides composed of: SG1, SG2, SG3, SG4, SG5, SG6, SG7,
SG8, SG9, SG10, SG11, SG12, SG13, SG14, SG15, SG16, SG17, SG18,
SG19, SG20, SG21, SG22, SG23, SG24, SG25, SG26, SG27, SG28, SG29,
SG30, SG31, SG32, SG33, SG34, SG35, SG36, SG37, SG38, SG39, SG40,
SG41, SG42, SG43, SG44, SG45, SG46, SG47, SG48, SG49, SG50, SG51,
SG52, SG53, SG54, SG55, SG56, SG57, SG58, SG59, SG60, SG61, SG62,
SG63, SG64, SG65, SG66, SG67, SG68, SG69, SG70, SG71, SG72, SG73,
SG74, SG75, SG76, SG77, SG78, SG79, SG80, SG81, SG82, SG83, SG84,
SG85, SG86, SG87, SG88, SG89, SG90, SG91, SG92, SG93, SG94, SG95,
SG96, SG97, SG98, SG99, SG100, SG101, SG102, SG103, SG104, SG105,
SG106, SG107, SG108, SG109, SG110, SG111, SG112, SG113, SG114,
SG115, SG116, SG117, SG118, SG119, SG120, SG121, SG122, SG123,
SG124, SG125, SG126, SG127, SG128, SG129, SG130, SG131, SG132,
SG133, SG134, SG135, SG136, SG137, SG138, SG139, SG140, SG141,
SG142, SG143, SG144, SG145, SG146, SG147, SG148, SG149, SG150,
SG151, SG152, SG153, SG154, SG155, SG156, SG157, SG158, SG159,
SG160, SG161, SG162, SG163, SG164, SG165, SG166, SG167, SG168,
SG169, SG170, SG171, SG172, SG173, SG174, SG175, SG176, SG177,
SG178, SG179, SG180, SG181, SG182, SG183, SG184, SG185, SG186,
SG187, SG188, SG189, SG190, SG191, SG192, SG193, SG194, SG195,
SG196, SG197, SG198, SG199, SG200, SG201, SG202, SG203, SG204,
SG205, SG206, SG207, SG208, SG209, SG210, SG211, SG212, SG213,
SG214, SG215, SG216, SG217, SG218, SG219, SG220, SG221, SG222,
SG223, SG224, SG225, SG226, SG227, SG228, SG229, SG230, SG231,
SG232, SG233, SG234, SG235, SG236, SG237, SG238, SG239, SG240,
SG241, SG242, SG243, SG244, SG245, SG246, SG247, SG248, SG249,
SG250, SG251, SG252, SG253, SG254, SG255, SG256, SG257, SG258,
SG259, SG260, SG261, SG262, SG263, SG264, SG265, SG266, SG267,
SG268, SG269, SG270, SG271, SG272, SG273, SG274, SG275, SG276,
SG277, SG278, SG279, SG280, SG281, SG282, SG283, SG284, SG285,
SG286, SG287, SG288, SG289, SG290, SG291, SG292, SG293, SG294,
SG295, SG296, SG297, SG298, SG299, SG300, SG301, SG302, SG303,
SG304, SG305, SG306, SG307, SG308, SG309, SG310, SG311, SG312,
SG313, SG314, SG315, SG316, SG317, SG318, SG319, SG320, SG321,
SG322, SG323, SG324, SG325, SG326, SG327, SG328, SG329, SG330,
SG331, SG332, SG333, SG334, SG335, SG336, SG337, SG338, SG339,
SG340, SG341, SG342, SG343, SG344, SG345, SG346, SG347, SG348,
SG349, SG350, SG351, SG352, SG353, SG354, SG355, SG356, SG357,
SG358, SG359, SG360, SG361, SG362, SG363, SG364, SG365, SG366,
SG367, SG368, SG369, SG370, SG371, SG372, SG373, SG374, SG375,
SG376, SG377, SG378, SG379, SG380, SG381, SG382, SG383, SG384,
SG385, SG386, SG387, SG388, SG389, SG390, SG391, SG392, SG393,
SG394, SG395, SG396, SG397, SG398, SG399, SG400, SG401, SG402,
SG403, SG404, SG405, SG406, SG407, SG408, SG409, SG410, SG411,
SG412, SG413, SG414, SG415, SG416, SG417, SG418, SG419, SG420,
SG421, SG422, SG423, SG424, SG425, SG426, SG427, SG428, SG429,
SG430, SG431, SG432, SG433, SG434, SG435, SG436, SG437, SG438,
SG439, SG440, SG441, SG442, SG443, SG444, SG445, SG446, SG447,
SG448, SG449, SG450, SG451, SG452, SG453, SG454, SG455, SG456,
SG457, SG458, SG459, SG460, SG461, SG462, SG465, SG468, SG469,
SG470, SG471, SG472, SG473, SG474, SG475, SG476, SG477, SG478,
SG479, SG480, SG481, SG482, SG483, SG484, SG485, SG486, SG487,
SG488, SG489, SG490, SG491, SG492, SG493, SG494, SG495, SG496,
SG497, SG498, SG499, SG500, SG501, SG502, SG503, SG504, SG505,
SG506, SG507, SG508, SG509, SG510, SG511, SG512, SG513, SG514,
SG515, SG516, SG517, SG518, SG519, SG520, SG521, SG522, SG523,
SG524, SG525, SG526, SG527, SG428, SG529, SG530, SG531, SG532,
SG533, SG534, SG535, SG536, SG537, SG538, SG539, SG540, SG541,
SG542, SG543, SG544, SG545, SG546, SG547, SG548, SG549, SG550,
SG551, SG552, SG553, SG554, SG555, SG556, SG557, SG558, SG559,
SG560, SG561, SG562, SG563, or combinations thereof.
27. Method for the in vitro diagnosis of a neoplasia originating
from hematopoietic cells and/or the in vitro prognosis of the
evolution thereof according to claim 26, which additionally
comprises a previous optional step of identification of genes
significant for the classification of a sample as associated or not
to a specific type of neoplasia originating from hematopoietic
cells, a previous step which comprises the substeps of: a) deciding
the possible categories wherein the sample can be classified; b)
obtaining biological samples from individuals which have previously
been assigned by a method different to that claimed to any of the
possible classification categories, so that there are samples of
each one of the possible categories; c) obtaining the total mRNA of
each one of the samples; d) obtaining the corresponding total cRNA,
labelled by a method which allows its subsequent detection, of at
least one aliquot of each one of the samples of mRNA, an aliquot
whereto is added before the obtainment of the cRNA at least one
sequence of polyadenylated nucleotides of low homology with human
genes for which it acts as internal positive control of the
process; e) adding to one of the aliquots of cRNA which are going
to be used in step f) at least one oligonucleotide of low homology
with human genes different from and not complementary to any
possible sequence of nucleotides which have been added in step d),
for which it acts as positive hybridization control; f)
hybridizing, in strict conditions, at least one aliquot of total
cRNA of each one of the samples with at least one microarray which
comprises at least two copies of each one of the oligonucleotides
from the group composed of: SG1, SG2, SG3, SG4, SG5, SG6, SG7, SG8,
SG9, SG10, SG11, SG12, SG13, SG14, SG15, SG16, SG17, SG18, SG19,
SG20, SG21, SG22, SG23, SG24, SG25, SG26, SG27, SG28, SG29, SG30,
SG31, SG32, SG33, SG34, SG35, SG36, SG37, SG38, SG39, SG40, SG41,
SG42, SG43, SG44, SG45, SG46, SG47, SG48, SG49, SG50, SG51, SG52,
SG53, SG54, SG55, SG56, SG57, SG58, SG59, SG60, SG61, SG62, SG63,
SG64, SG65, SG66, SG67, SG68, SG69, SG70, SG71, SG72, SG73, SG74,
SG75, SG76, SG77, SG78, SG79, SG80, SG81, SG82, SG83, SG84, SG85,
SG86, SG87, SG88, SG89, SG90, SG91, SG92, SG93, SG94, SG95, SG96,
SG97, SG98, SG99, SG100, SG101, SG102, SG103, SG104, SG105, SG106,
SG107, SG108, SG109, SG110, SG111, SG112, SG113, SG114, SG115,
SG116, SG117, SG118, SG119, SG120, SG121, SG122, SG123, SG124,
SG125, SG126, SG127, SG128, SG129, SG130, SG131, SG132, SG133,
SG134, SG135, SG136, SG137, SG138, SG139, SG140, SG141, SG142,
SG143, SG144, SG145, SG146, SG147, SG148, SG149, SG150, SG151,
SG152, SG153, SG154, SG155, SG156, SG157, SG158, SG159, SG160,
SG161, SG162, SG163, SG164, SG165, SG166, SG167, SG168, SG169,
SG170, SG171, SG172, SG173, SG174, SG175, SG176, SG177, SG178,
SG179, SG180, SG181, SG182, SG183, SG184, SG185, SG186, SG187,
SG188, SG189, SG190, SG191, SG192, SG193, SG194, SG195, SG196,
SG197, SG198, SG199, SG200, SG201, SG202, SG203, SG204, SG205,
SG206, SG207, SG208, SG209, SG210, SG211, SG212, SG213, SG214,
SG215, SG216, SG217, SG218, SG219, SG220, SG221, SG222, SG223,
SG224, SG225, SG226, SG227, SG228, SG229, SG230, SG231, SG232,
SG233, SG234, SG235, SG236, SG237, SG238, SG239, SG240, SG241,
SG242, SG243, SG244, SG245, SG246, SG247, SG248, SG249, SG250,
SG251, SG252, SG253, SG254, SG255, SG256, SG257, SG258, SG259,
SG260, SG261, SG262, SG263, SG264, SG265, SG266, SG267, SG268,
SG269, SG270, SG271, SG272, SG273, SG274, SG275, SG276, SG277,
SG278, SG279, SG280, SG281, SG282, SG283, SG284, SG285, SG286,
SG287, SG288, SG289, SG290, SG291, SG292, SG293, SG294, SG295,
SG296, SG297, SG298, SG299, SG300, SG301, SG302, SG303, SG304,
SG305, SG306, SG307, SG308, SG309, SG310, SG311, SG312, SG313,
SG314, SG315, SG316, SG317, SG318, SG319, SG320, SG321, SG322,
SG323, SG324, SG325, SG326, SG327, SG328, SG329, SG330, SG331,
SG332, SG333, SG334, SG335, SG336, SG337, SG338, SG339, SG340,
SG341, SG342, SG343, SG344, SG345, SG346, SG347, SG348, SG349,
SG350, SG351, SG352, SG353, SG354, SG355, SG356, SG357, SG358,
SG359, SG360, SG361, SG362, SG363, SG364, SG365, SG366, SG367,
SG368, SG369, SG370, SG371, SG372, SG373, SG374, SG375, SG376,
SG377, SG378, SG379, SG380, SG381, SG382, SG383, SG384, SG385,
SG386, SG387, SG388, SG389, SG390, SG391, SG392, SG393, SG394,
SG395, SG396, SG397, SG398, SG399, SG400, SG401, SG402, SG403,
SG404, SG405, SG406, SG407, SG408, SG409, SG410, SG411, SG412,
SG413, SG414, SG415, SG416, SG417, SG418, SG419, SG420, SG421,
SG422, SG423, SG424, SG425, SG426, SG427, SG428, SG429, SG430,
SG431, SG432, SG433, SG434, SG435, SG436, SG437, SG438, SG439,
SG440, SG441, SG442, SG443, SG444, SG445, SG446, SG447, SG448,
SG449, SG450, SG451, SG452, SG453, SG454, SG455, SG456, SG457,
SG458, SG459, SG460, SG461, SG462, SG465, SG468, SG469, SG470,
SG471, SG472, SG473, SG474, SG475, SG476, SG477, SG478, SG479,
SG480, SG481, SG482, SG483, SG484, SG485, SG486, SG487, SG488,
SG489, SG490, SG491, SG492, SG493, SG494, SG495, SG496, SG497,
SG498, SG499, SG500, SG501, SG502, SG503, SG504, SG505, SG506,
SG507, SG508, SG509, SG510, SG511, SG512, SG513, SG514, SG515,
SG516, SG517, SG518, SG519, SG520, SG521, SG522, SG523, SG524,
SG525, SG526, SG527, SG428, SG529, SG530, SG531, SG532, SG533,
SG534, SG535, SG536, SG537, SG538, SG539, SG540, SG541, SG542,
SG543, SG544, SG545, SG546, SG547, SG548, SG549, SG550, SG551,
SG552, SG553, SG554, SG555, SG556, SG557, SG558, SG559, SG560,
SG561, SG562, SG563, a microarray which additionally comprises: a.
at least two points which correspond to different aliquots of the
solvent wherein nucleotides are found at the time of their deposit
on the surface of the microarray, for which they serve as blank, b.
at least two copies of at least one oligonucleotide for each one of
the polyadenylated sequences added in step d), an oligonucleotide
whose sequence will correspond to a fragment, different from the
polyadenylation zone, of the sequence of polyadenylated nucleotides
whose evolution in the process has to be controlled; c. for each
one of the oligonucleotides added in step e), at least two copies
of an oligonucleotide complementary thereto; d. at least two copies
of each member of at least one pair of oligonucleotides wherein the
sequence of one of the members corresponds to a sequence of zone 5'
and the sequence of the other corresponds to a sequence of zone 3'
of the mRNA of a gene which is expressed in constitutive form in
any cell of hematopoietic origin; e. at least two copies of at
least one oligonucleotide of low homology with human genes
different from any of the oligonucleotides defined in section b.
and different from any of the synthetic oligonucleotides added
optionally in step e); g) detecting and quantifying the signal of
cRNA hybridized with each one of the copies of each one of the
oligonucleotides present in the microarray, as well as the signal
corresponding to the points of the solvent; h) calculating the
average level of intensity of hybridization of each one of the
oligonucleotides of the microarray calculating the average of the
intensities of the copies of each one of the oligonucleotides; i)
taking the hybridization as valid if the following conditions are
complied with: a. the ratio between the average intensity and the
average background of all the oligonucleotides of the microarray is
greater than 10; b. the value of the average coefficient of
variation of all the replicas of oligonucleotides should be less
than 0.3; c. the average value of negative control should be less
than 2.5 times the average value of the points corresponding to the
solvent; d. there is a signal both in the hybridization controls
and in the internal positive controls used as process control; j)
normalizing the data; k) eliminating the oligonucleotides with
values of average intensity minus average background noise less
than approximately 2 times the average value obtained with the
points corresponding to the solvent, as well as the
oligonucleotides with an interquartile range of normalized
intensity throughout the samples less than 0.3; l) performing the
statistical analysis to find the statistically significant
oligonucleotides to differentiate between the different categories
and be able to classify a sample which has not been previously
assigned to any category, choosing said oligonucleotides among
those which have not been eliminated in the previous steps, until
obtaining "n" oligonucleotides which either have a value of p less
than a limit which is chosen from the open range of 0 to 0.05,
preferably using for it a method with capacity to reduce false
positives, or that which best defines the category established; m)
checking that the grouping of the samples according to the
differences in intensities between the different samples detected
for the statistically significant oligonucleotides gives rise to
the samples being classified in the same categories as those which
had previously been assigned by a different method.
28. Method according to claim 27, wherein the microarray comprises
at least four copies of each one of the oligonucleotides present in
it and the average of the intensities of the copies of each one of
the oligonucleotides which is calculated in h) is a trimmed
mean.
29. Method according to claim 28, wherein the normalization is
carried out using the "variance stabilization normalization" method
available in the "vsn" package in R.
30. Method according to claim 27, wherein the statistical analysis
to find the statistically significant oligonucleotides to
differentiate between the different categories is carried out using
the mt.maxT function of the multtest package in R.
31. Method according to claim 27, wherein the diagnosis is done
with a diagnostic device which comprises a composition containing
at least one oligonucleotide from the group composed of: SG1, SG2,
SG3, SG4, SG5, SG6, SG7, SG8, SG9, SG10, SG11, SG12, SG13, SG14,
SG15, SG16, SG17, SG18, SG19, SG20, SG21, SG22, SG23, SG24, SG25,
SG26, SG27, SG28, SG29, SG30, SG31, SG32, SG33, SG34, SG35, SG36,
SG37, SG38, SG39, SG40, SG41, SG42, SG43, SG44, SG45, SG46, SG47,
SG48, SG49, SG50, SG51, SG52, SG53, SG54, SG55, SG56, SG57, SG58,
SG59, SG60, SG61, SG62, SG63, SG64, SG65, SG66, SG67, SG68, SG69,
SG70, SG71, SG72, SG73, SG74, SG75, SG76, SG77, SG78, SG79, SG80,
SG81, SG82, SG83, SG84, SG85, SG86, SG87, SG88, SG89, SG90, SG91,
SG92, SG93, SG94, SG95, SG96, SG97, SG98, SG99, SG100, SG101,
SG102, SG103, SG104, SG105, SG106, SG107, SG108, SG109, SG110,
SG111, SG112, SG113, SG114, SG115, SG116, SG117, SG118, SG119,
SG120, SG121, SG122, SG123, SG124, SG125, SG126, SG127, SG128,
SG129, SG130, SG131, SG132, SG133, SG134, SG135, SG136, SG137,
SG138, SG139, SG140, SG141, SG142, SG143, SG144, SG145, SG146,
SG147, SG148, SG149, SG150, SG151, SG152, SG153, SG154, SG155,
SG156, SG157, SG158, SG159, SG160, SG161, SG162, SG163, SG164,
SG165, SG166, SG167, SG168, SG169, SG170, SG171, SG172, SG173,
SG174, SG175, SG176, SG177, SG178, SG179, SG180, SG181, SG182,
SG183, SG184, SG185, SG186, SG187, SG188, SG189, SG190, SG191,
SG192, SG193, SG194, SG195, SG196, SG197, SG198, SG199, SG200,
SG201, SG202, SG203, SG204, SG205, SG206, SG207, SG208, SG209,
SG210, SG211, SG212, SG213, SG214, SG215, SG216, SG217, SG218,
SG219, SG220, SG221, SG222, SG223, SG224, SG225, SG226, SG227,
SG228, SG229, SG230, SG231, SG232, SG233, SG234, SG235, SG236,
SG237, SG238, SG239, SG240, SG241, SG242, SG243, SG244, SG245,
SG246, SG247, SG248, SG249, SG250, SG251, SG252, SG253, SG254,
SG255, SG256, SG257, SG258, SG259, SG260, SG261, SG262, SG263,
SG264, SG265, SG266, SG267, SG268, SG269, SG270, SG271, SG272,
SG273, SG274, SG275, SG276, SG277, SG278, SG279, SG280, SG281,
SG282, SG283, SG284, SG285, SG286, SG287, SG288, SG289, SG290,
SG291, SG292, SG293, SG294, SG295, SG296, SG297, SG298, SG299,
SG300, SG301, SG302, SG303, SG304, SG305, SG306, SG307, SG308,
SG309, SG310, SG311, SG312, SG313, SG314, SG315, SG316, SG317,
SG318, SG319, SG320, SG321, SG322, SG323, SG324, SG325, SG326,
SG327, SG328, SG329, SG330, SG331, SG332, SG333, SG334, SG335,
SG336, SG337, SG338, SG339, SG340, SG341, SG342, SG343, SG344,
SG345, SG346, SG347, SG348, SG349, SG350, SG351, SG352, SG353,
SG354, SG355, SG356, SG357, SG358, SG359, SG360, SG361, SG362,
SG363, SG364, SG365, SG366, SG367, SG368, SG369, SG370, SG371,
SG372, SG373, SG374, SG375, SG376, SG377, SG378, SG379, SG380,
SG381, SG382, SG383, SG384, SG385, SG386, SG387, SG388, SG389,
SG390, SG391, SG392, SG393, SG394, SG395, SG396, SG397, SG398,
SG399, SG400, SG401, SG402, SG403, SG404, SG405, SG406, SG407,
SG408, SG409, SG410, SG411, SG412, SG413, SG414, SG415, SG416,
SG417, SG418, SG419, SG420, SG421, SG422, SG423, SG424, SG425,
SG426, SG427, SG428, SG429, SG430, SG431, SG432, SG433, SG434,
SG435, SG436, SG437, SG438, SG439, SG440, SG441, SG442, SG443,
SG444, SG445, SG446, SG447, SG448, SG449, SG450, SG451, SG452,
SG453, SG454, SG455, SG456, SG457, SG458, SG459, SG460, SG461,
SG462, SG465, SG468, SG469, SG470, SG471, SG472, SG473, SG474,
SG475, SG476, SG477, SG478, SG479, SG480, SG481, SG482, SG483,
SG484, SG485, SG486, SG487, SG488, SG489, SG490, SG491, SG492,
SG493, SG494, SG495, SG496, SG497, SG498, SG499, SG500, SG501,
SG502, SG503, SG504, SG505, SG506, SG507, SG508, SG509, SG510,
SG511, SG512, SG513, SG514, SG515, SG516, SG517, SG518, SG519,
SG520, SG521, SG522, SG523, SG524, SG525, SG526, SG527, SG428,
SG529, SG530, SG531, SG532, SG533, SG534, SG535, SG536, SG537,
SG538, SG539, SG540, SG541, SG542, SG543, SG544, SG545, SG546,
SG547, SG548, SG549, SG550, SG551, SG552, SG553, SG554, SG555,
SG556, SG557, SG558, SG559, SG560, SG561, SG562, SG563, or
combinations thereof, to be used as probe in the determination of
the expression level of a gene which possesses a sequence
complementary to said oligonucleotide by the evaluation of the mRNA
level corresponding to that gene, of application in the in vitro
diagnosis of neoplasias originating from hematopoietic cells and/or
in the in vitro prognosis of the evolution of said disease.
32. Method according to claim 27, which comprises an optional step
of obtainment of a classification function for each sample by the
arbitrary assignment of the value of 0 to one of the possible
categories "a" and of the value 1 to the other possible category
"b" wherein it is possible to classify the sample and the
obtainment by logistical regression of a coefficient for each one
of the oligonucleotides which make it possible to calculate a value
x.sub.i for each sample by a function of the type: n
x.sub.i=constant+.SIGMA.(coeff_olig.sub.m*Imn.sub.i.sub.--olig.sub.m)
m=1 where coeff_olig.sub.m represents the coefficient calculated
for a specific oligonucleotide Imn.sub.i.sub.--olig.sub.m
represents the average value of normalized intensity obtained in
the hybridization of the sample i calculated for the
oligonucleotide "m" varies from 1 to "n" n is the total number of
oligonucleotides considered significant value "x.sub.i" wherefrom
the probability "p.sub.i" that a sample "i" belongs to one or
another category is calculated using the formula
p.sub.i=1/(1+e.sup.-xi) and classifying the sample as belonging to
category "a" or "b" according to its corresponding value p.sub.i is
closer to 0 or 1, respectively.
33. Method according to claim 27, wherein the statistical analysis
to find the significant oligonucleotides to differentiate between
the different categories is carried out using the "Nearest Shrunken
Centroids" method.
34. Method according to claim 27, wherein the biological samples
analysed in vitro are samples of peripheral blood.
35. Method according to claim 34, wherein a leukemia is diagnosed
in vitro or a prognosis is made of the evolution thereof.
36. Method according to claim 35, wherein it is diagnosed in vitro
if an individual suffers from chronic lymphatic leukemia.
37. Method according to claim 35, wherein an in vitro prognosis is
made of the evolution of the chronic lymphatic leukemia in a
subject classifying a sample of blood extracted therefrom as
"associated to stable chronic lymphatic leukemia" or as "associated
to progressive chronic lymphatic leukemia".
38. Method to make an in vitro diagnosis of a neoplasia originating
from hematopoietic cells and/or an in vitro prognosis of the
evolution thereof which comprises the in vitro detection and the
statistical analysis of the expression level of at least one
significant gene for classifying the sample as belonging to a
healthy individual or associating it to a type of neoplasia
originating from hematopoietic cells according to claim 26, wherein
the neoplasia which is diagnosed and/or whose evolution a prognosis
is made of is a leukemia.
39. Method according to claim 38, wherein a diagnosis/or prognosis
is made of the evolution of the chronic lymphatic leukemia.
40. Method to make an in vitro diagnosis of chronic lymphatic
leukemia and/or make an in vitro prognosis of its evolution
according to claim 39, wherein the in vitro detection of the
expression level of at least one significant gene is carried out
from samples of peripheral blood.
41. Method to make an in vitro diagnosis of chronic lymphatic
leukemia according to claim 40, wherein the subjects wherefrom the
corresponding blood samples have been taken are classified in the
category of subject not suffering from CLL or in the category of
subject suffering from CLL.
42. Method to make an in vitro diagnosis of chronic lymphatic
leukemia according to claim 41, wherein the classification of the
subjects is carried out after the in vitro detection and the
statistical analysis of the expression level in the corresponding
blood samples of at least genes CD79A, FAIM3, HLA-DRA, HLA-DRB3,
HLA-DQA1.
43. Method to make an in vitro diagnosis of chronic lymphatic
leukemia according to claim 42, wherein the classification of the
subjects is carried out after the in vitro detection and the
statistical analysis of the expression level in the corresponding
blood samples additionally of genes IRF8 and COL3A1.
44. Method to make an in vitro diagnosis of chronic lymphatic
leukemia according to claim 43, wherein the in vitro detection and
the statistical analysis of the expression level of genes CD79A,
FAIM3, HLA-DRA, HLA-DRB3, HLA-DQA1, IRF8 and COL3A1 is carried out
by the evaluation of the corresponding mRNA by hybridization of its
corresponding cRNA using as probes the oligonucleotides SG117,
SG428, SG459, SG507, SG508, SG461 and SG493.
45. Method to make an in vitro diagnosis of chronic lymphatic
leukemia according to claim 44, wherein the oligonucleotides form
part of a composition in the form of microarray.
46. Method to make an in vitro diagnosis of chronic lymphatic
leukemia according to claim 45, wherein the evaluation of the
hybridized cRNA is carried out thanks to the prior labelling of
cRNA with biotin, the staining of the hybridized microarray with
streptavidin conjugated with a fluorophore and the detection of the
signal emitted by said fluorophore.
47. Method to make an in vitro diagnosis of chronic lymphatic
leukemia according to claim 46, wherein the fluorophore is Cy3.
48. Method to make an in vitro diagnosis of chronic lymphatic
leukemia according to claim 47, wherein the classification of a
subject from which the sample I has been taken analysed in the
category of subject not suffering from CLL or in the category of
subject suffering from CLL is carried out by calculating for said
subject a value of probability p, =1/(1+e.sup.-xi) after obtaining
its corresponding value of x.sub.i by the formula
x.sub.i=-719.241486+(2.44756372*Imn.sub.i.sub.--CD79A)+(7.38657611*Imn.su-
b.i.sub.--FAIM3)+(23.1465464*Imn.sub.i.sub.--HLA-DRA)+(43.6287742*Imn.sub.-
i.sub.--IRF8)-(19.3978182*Imn.sub.i.sub.--COL3A1)-(2.80282646*Imn.sub.i.su-
b.--HLA-DRB3)+(49.5345672*Imn.sub.i.sub.--HLA-DQA1) formula wherein
each one of the values called abbreviation "Imn.sub.i" followed by
the abbreviation of a gene makes reference to the average value of
normalized intensity obtained after detecting the hybridization
signal corresponding to the oligonucleotide which is being used as
probe to evaluate the expression of the said gene and classifying
the subject as subject not suffering from CLL if the value of
p.sub.i is less than 0.5 and as subject suffering from CLL if the
value of p.sub.i is greater than 0.5.
49. Method to make an in vitro prognosis of the evolution of the
disease in a subject suffering from chronic lymphatic leukemia
according to claim 40, wherein the subjects from which the
corresponding blood samples have been taken are classified in the
category of subject with stable CLL or in the category of subject
with progressive CLL.
50. Method to make an in vitro prognosis of the evolution of the
disease in a subject suffering from chronic lymphatic leukemia
according to claim 49, wherein the classification of the subjects
is carried out after the in vitro detection and the statistical
analysis of the expression level in the corresponding blood samples
of at least genes PSMB4, FCER2 and POU2F2.
51. Method to make an in vitro prognosis of the evolution of the
disease in a subject suffering from chronic lymphatic leukemia
according to claim 50, wherein the classification of the subjects
is carried out after the in vitro detection and the statistical
analysis of the expression level in the corresponding blood samples
additionally of at least one gene selected from the group composed
of ODC1, CD79A, CD2, CD3E, CD5, MS4A1, EIF4E, FHIT, NR3C1, LCP1,
MAPK10, ABCC5, XRCC3, CML66, PLZF, RBP4.
52. Method to make an in vitro prognosis of the evolution of the
disease in a subject suffering from chronic lymphatic leukemia
according to claim 51, wherein the classification of the subjects
is carried out after the in vitro detection and the statistical
analysis of the expression level in the corresponding blood samples
of at least the genes of the group composed of PSMB4, FCER2,
POU2F2, ODC1, CD79A, CD2, CD3E, CD5, MS4A1, EIF4E, FHIT, NR3C1,
LCP1, MAPK10, ABCC5, XRCC3, CML66, PLZF, RBP4.
53. Method to make an in vitro prognosis of the evolution of the
disease in a subject suffering from chronic lymphatic leukemia
according to either of claims 51, wherein the in vitro detection
and the statistical analysis of the expression level of the genes
examined is carried out by the evaluation of the corresponding mRNA
by hybridization of its corresponding cRNA using as probes the
corresponding oligonucleotides selected from the group composed of
SG26, SG216, SG366, SG31, SG177, SG194, SG195, SG197, SG213, SG293,
SG301, SG309, SG33, SG343, SG357, SG439, SG452, SG555, SG556.
54. Method to make an in vitro prognosis of the evolution of the
disease in a subject suffering from chronic lymphatic leukemia
according to claim 53, wherein the oligonucleotides form part of a
composition in the form of microarray.
55. Method to make an in vitro prognosis of the evolution of the
disease in a subject suffering from chronic lymphatic leukemia
according to claim 54, wherein the evaluation of the corresponding
mRNA of the sample analysed by the detection of the corresponding
hybridized cRNA to the corresponding oligonucleotide is carried out
thanks to the previous labelling of the cRNA with biotin, the
staining of the microarray hybridized with streptavidin conjugated
with a fluorophore and the detection of the signal emitted by said
fluorophore.
56. Method to make an in vitro prognosis of the evolution of the
disease in an individual suffering from chronic lymphatic leukemia
according to claim 55, wherein the fluorophore is Cy3.
57. A method comprising use of a device for evaluation of the
expression level of at least one gene of the group composed of
PSMB4, FCER2, POU2F2, ODC1, CD79A, CD2, CD3E, CD5, MS4A1, EIF4E,
FHIT, NR3C1, LCP1, MAPK10, ABCC5, XRCC3, CML66, PLZF, RBP4, CD79A,
FAIM3, HLA-DRA, HLA-DRB3, HLA-DQA1, IRF8 and COL3A1 for the in
vitro diagnosis of the existence of chronic lymphatic leukemia in a
subject and/or for the in vitro prognosis of the evolution of the
chronic lymphatic leukemia in a subject.
58. A method comprising use of a device for evaluation of the
expression level of genes according to claim 57, wherein the
expression level of at least one gene of the group composed of
CD79A, FAIM3, HLA-DRA, HLA-DRB3, HLA-DQA1, IRF8 and COL3A1 is
evaluated for the in vitro diagnosis of the existence of chronic
lymphatic leukemia in a subject.
59. A method comprising use of a device for evaluation of the
expression level of genes according to claim 57, wherein the
expression level of at least genes CD79A, FAIM3, HLA-DRA, HLA-DRB3,
HLA-DQA1 is evaluated for the in vitro diagnosis of the existence
of chronic lymphatic leukemia in a subject.
60. A method comprising use of a device for evaluation of the
expression level of genes according to claim 59, wherein
additionally the expression level of at least genes IRF8 and COL3A1
are evaluated for the in vitro diagnosis of the existence of
chronic lymphatic leukemia in a subject.
61. A method comprising use of a device for evaluation of the
expression level of genes according to claim 57, wherein the
expression level of at least one gene of the group composed of
PSMB4, FCER2, POU2F2, ODC1, CD79A, CD2, CD3E, CD5, MS4A1, EIF4E,
FHIT, NR3C1, LCP1, MAPK10, ABCC5, XRCC3, CML66, PLZF, RBP4 is
evaluated, to make an in vitro prognosis of the evolution of the
disease in a subject suffering from chronic lymphatic leukemia.
Description
FIELD OF THE INVENTION
[0001] The invention relates to the technical-industrial sector of
the extracorporeal in vitro diagnosis of biological samples, by
genetic engineering techniques, applied to the diagnosis of
specific types of neoplasias from their gene expression patterns
and/or to the prognosis of their evolution. More specifically, the
invention relates to the identification of neoplasias originating
from hematopoietic cells from the evaluation of the levels of
messenger RNA of significant genes in biological samples such as
peripheral blood samples, preferably by the use of microarrays.
With this it is possible to identify samples corresponding to
patients suffering from CLL, permitting the diagnosis thereof and,
furthermore, it is possible to classify samples from patients
suffering from CLL in samples which belong to patients wherein the
CLL is going to remain stable or wherein it is going to progress,
enabling the prognosis of the future evolution of these
patients.
BACKGROUND OF THE INVENTION
[0002] Each day, the human body produces billions of new white and
red cells and platelets which replace the hematopoietic cells which
are lost as a consequence of a normal process of renewal, disease
or trauma. The organized production process of hematopoietic cells
and homeostasis is known with the name of hematopoiesis (Weissman I
L et al., 2000; Leung A Y H et al., 2005.
[0003] In man, hematopoiesis is confined to the bone marrow (B.M.)
of the greater part of the bones, and gradually, with age, this is
replaced by fat, which in the adult, 70% of the bone marrow is
located in the pelvis, vertebra and sternum (Bernard et al.,
1976).
[0004] All the mature blood cells are generated from a relatively
low number of hematopoietic cells known hematopoietic stem cells.
The hematopoietic stem cell has two characteristics which are the
pluripotentiality or capacity to give rise to different
hematopoietic cell strains and the self-renewal or property of
self-perpetuation, generating cells the same as its self (Weissman
I L et al., 2000). This capacity is essential for the maintenance
of hematopoiesis throughout the life which, without self-renewal,
would quickly exhaust the reserve of available stem cells.
Hematopoietic stem cells are capable of generating different mature
hematopoietic cell types through a series of intermediate
progenitors and precursors. These progenitors and precursors suffer
an ordered sequence of events which transform them into mature
cells. This process is known with the name of differentiation (Lee
M F et al., 2005). The differentiation of the hematopoietic cells
involves changes which affect, among others, the size and form of
the cell, gene expression, proteins, response to signals and
localization of the cells.
[0005] The terminally differentiated cells have lost their capacity
for division and suffer apoptosis after a period of time which goes
from hours for neutrophils to decades for some lymphocytes. This
fact means the B.M. should constantly ensure cell exchange (Datta S
R et al., 1999).
[0006] The hematopoiesis process comprises a complex interaction
between intrinsic genetic events of the hematopoietic cells and
environment wherein they are found. This interaction is that which
determines if the hematopoietic precursors and progenitors must
stay quiescent, proliferate, be differentiated in one or another
line or enter into apoptosis (Domen J et al., 1999). All the
genetic and environmental mechanisms which govern the production of
blood cells operate by altering the relative balance of these
fundamental cell processes.
[0007] Environmental and genetic factors are critical in
hematopoiesis. Thus, for example, the gene expression belongings to
the Rb families (Bergh et al., 1999), cyclins (Della Ragione F et
al., 1997) or Hox (Magli M C et al., 1997) regulate the
proliferation of hematopoietic cells at early stages of
differentiation. The genes of the bcl-2 family regulate apoptosis
in hematopoietic cells (O'Gorman D M et al., 2001). A great variety
of genes among which are found C/EBP (Tenen D G et al., 1997), Pax5
(Nutt S L et al., 1999) and lkaros (Nichogiannopoulou A. et al.,
1998) seem to be involved in hematopoietic differentiation and line
compromise.
Hematological Neoplasias
[0008] Hematological neoplasias are malignant processes which
affect any one of the cell types involved in the hematopoietic
system. As a consequence of this transformation, the cell is
blocked in a stage of differentiation and starts to accumulate due
to uncontrolled proliferation, to a failure of the apoptotic
mechanisms or a blocking of its differentiation process.
[0009] The malignant transformation of the hematopoietic cells
during the different stages they pass through in their
differentiation to mature cells originates a great number of
different neoplasias (Guttmacher A E et al., 2003). This type of
neoplasias is therefore a very heterogeneous group of diseases
which only has the hematopoietic origin of the cell type
transformed in common.
Classification of Hematological Neoplasias
[0010] Generically, it is possible to establish two groups:
lymphoid neoplasias which affect the different cell type and
degrees of maturity which form the lymphoid line, both B and T, and
the other large group is constituted by the myeloid neoplasis which
affect various cell types of the myeloid line. However, this
simplistic classification is currently more developed, as detailed
below.
[0011] From a clinical standpoint, classically, lymphoma leukemias
have been differentiated in arbitrary form, indicating the
leukemias as those neoplasias which affect the bone marrow and have
peripheral expression, i.e. circulation of anomalous cells in
blood, and lymphomas as those neoplasias which remain localized in
the lymph nodes or other lymphoid tissues and which lack, at least
initially, leukemic behaviour. In the case of leukemias, the acute
processes of the chronics has initially been differentiated by the
morpho-cytological characteristics of the proliferating cells
(immature and atypical in the first case and differentiated in the
second) and to the clinical manifestations of the disease. At
present, the knowledge of the immunological markers and the genetic
alterations which affect the hematopoietic cells help to
differentiate the different processes more accurately.
[0012] Today, it is known that hematological neoplasias, as occurs
in other types of cancer, have a multigenic origin. The great
technological revolution produced in recent years has made it
possible to know the molecular basis of several neoplasias. The use
of these techniques makes it possible to identify relevant genes in
human cancer, confirm the results obtained in basic research in
animal models, establish patters of susceptibility, more accurately
classify the neoplasias, improve the diagnosis of the disease,
identify new therapeutic targets and improve the therapeutic
selection for each patient.
[0013] Also, the diversity which exists between individuals is
important and has its clinical repercussion, based on the genetic
differences: if we are capable of recognising these genetic
differences, we will also be capable of advancing in discovering
toxicity and differences in response to treatment. (Westbrook C A
et al., 2005).
[0014] In 1995, the World Health Organization (WHO) in
collaboration with the European Hematology Association and
pathologists, clinicians and scientists throughout the world,
started a project in order to obtain an agreed classification of
the hematopoietic tissue and lymphoid organs. This project led to
the development of a system for the definition, classification and
establishment of agreed diagnostic criteria for myeloid, lymphoid
and histiocytic neoplasias (Jaffe E S et al., 2001). The
classification criteria of the WHO are the same used in the REAL
(Revised European American Lymphoma) classification published by
the International Lymphoma Study Group in 1994 (Harris N L et al.,
1994). The REAL classification system, unlike other previous
classification systems is based on the definition of "real"
entities and not morphological subtypes. All available information
is used to establish these "real" entities, i.e. morphological,
immunophenotypical and biological data are combined with the
genetic and clinical characteristics (Harris N L et al.,
1999a).
[0015] The WHO classification, which was presented in 1997,
stratifies the entities in accordance with the cell line affected:
myeloid, lymphoid, histiocytic/dentritic and mastocytic. Within
each category, the disease is defined in accordance with the
morphology, immunophenotype, genetic and clinical data (Harris N L
et al., 1999b). In many neoplasias, the stage wherein the
accumulated tumour cell is found does not coincide with the stage
in which the initial transformer event has occurred. Thus, many
hematological neoplasias originate in the initial precursors and
the specific genetic alteration may determine which cell continues
advancing in its differentiating until stopping and accumulating in
more advanced stages of differentiation (Shaffer A L et al., 2002).
In contrast, other neoplasias can develop in the more advanced
stages of differentiation, as occurs in the cells from the
follicular centres wherein the genetic translocations and
rearranging produce activation of genes which contribute to tumour
development. The classification for each entity reflects the best
stimulation for its cell line and stage of differentiation,
recognising that the knowledge available at present is imperfect
and that changes may occur in the assignment to a cell line and in
classification as the available knowledge improves.
[0016] The current criteria of diagnosis and classification of
these neoplasias are based on a combination of (Braziel R M et al,
2003): [0017] Morphological evaluation of the cell: Observation
under the microscope of the cells involved. Information is obtained
on the type of cell and degree of its maturity. [0018] Study of the
immunophenotype: Recognition of antigens expressed on the surface
of the neoplastic cell. These antigens are expressed differently
and to different degrees in accordance with the line and of the
stage the cell is at. The expression of surface antigens
characteristic of the line and stage of differentiation of the cell
is known, for example, the expression of CD19 and CD20 is typical
of line B cells, whilst the expression of CD3 is typical of line T.
The study of CD23 is key when differentiating NHLCM from CLL (Gong
J Z et al., 2001).
[0019] An attempt has always been made to relate the different
types of neoplasias with their corresponding normal cell population
through their morphological and immunophenotypical characteristics.
Many neoplasias therefore seem "trapped" in determined stages of
development as they have morphological and immunophenotypical
characteristics similar to those of the hematopoietic cell at that
stage of differentiation (Shaffer A L, et al., 2002). [0020]
Clinical characteristics: Signs and symptoms of the patient at the
time of diagnosis. [0021] Determination of molecular markers:
Measurement of some molecules which are associated to concrete
entities such as the presence of PMURARA in promyelocytic leukemia
or which give a better or worse prognosis, such as, for example,
the expression of CD38 in CLL cells marker of bad prognosis (Durig
J et al., 2002) [0022] Cytogenetic studies based on the search for
genetic alterations in the DNA of tumour cells. In many cases,
specific rearranging occur which are characteristic of types of
tumour or stages (Mitelman F, et al., 1997). In accordance with the
chromosome translocations, it is possible to establish different
groups with clinical significance, for example, in LLA-B, where the
presence of fusion oncoproteins is frequent, the presence of
t(2;21)/TEL1-AML1 and t(1;19)/E2A-PBX1 is associated with a
response to the treatment whilst the prognosis for patients with
t(9;22)/BCR-ABL and t(4;11)/MLL-AF4 is much worse (Arico M et al.,
2000). Searches are also usually made for specific mutations,
deletions or insertions in a gene which have been related to more
favourable prognosis such as, for example, the myelodysplastic
syndromes associated to 5q- (Boultwood J et al., 1994).
[0023] As has previously been commented, the WHO establishes four
large groups of hematological neoplasias in accordance with the
strain involved (myeloid, lymphoid, histiocytic/dentritic and
mastocytic lines). Below the neoplasias belonging to the myeloid
line and the lymphoid line are described in more detail as they are
those which arise with greatest frequency. Those corresponding to
the histiocytic/dentritic and mastocytic lines for the moment are
very isolated entities.
1. Myeloid Neoplasias
[0024] They group together all the neoplasias originated in the
myeloid line of differentiation, the WHO distinguishes four large
groups (Vardiman J W et al., 2002).
[0025] 1.1 Myeloproliferative Syndromes (MPS)
[0026] Myeloproliferative syndromes (MPS) are clonal alterations of
the hematopoietic stem cell characterized by effective
hematopoiesis which leads to an increase in the blood levels of one
or more hematopoietic and hepatosplenomegaly lines. They constitute
a group of entities wherein there exists an increase in precursors
of the myeloid series or fibrosis of the bone marrow
(myelofibrosis); this group also includes systemic mastocytosis.
The following can be highlighted: [0027] Chronic myeloproliferative
syndromes (CMPS). Clonal alteration of the hematopoeietic stem
cell. Characterized by an effective hematopoiesis which produces
increase in peripheral blood of one or more cell lines and
frequently hepatosplenomegaly, medullary hypercellularity with
maturity but without dysplasia. [0028] Chronic myeloid leukemia
(CML). It is a clonal process secondary to an acquired genetic
alteration of the pluripotent cell. The disease is characterized by
the superproduction of neu trophils and of their precursors. It has
three phases: the first called chronic phase of undefined duration,
followed by the acceleration phase and finally the blastic crisis
which is really secondary acute leukemia.
[0029] CML has a low incidence of approximately one case per
100,000 inhabitants/year and appears most frequently in the sixth
and seventh decades of life. It can be considered a rare
disease.
[0030] It is the characteristic leukemia par excellence as the term
leukaemia was applied to this entity for the first time. 95% of the
cases have a genetic marker, the Philadelphia chromosome,
originated by the translocation of a fragment of chromosome 22
which adheres to chromosome 9 or t(9;22) (q34;q11). This
translocation causes the fusion gene bcr-abl. The protein coded by
this chimeric gene, BCR-ABL, has an increased thyrosine-kinase
activity compared with the normal abl protein activity as oncogenic
growth factor (Pane F et al., 2002), although really the mechanisms
which produce the superproduction of myeloid cells are not totally
clarified. It is possible that other proto-oncogenes such as p-53
intervene in the process and in the transformation of chronic phase
to blastic crisis. The few cases in which the Philadelphia
chromosome is detected represent atypical myeloproliferative
symptoms and correspond to the variant of MDS known as chronic
myelomonocytic leukemia (CMML).
[0031] The diagnosis is based on the high cell counts for the blank
series, appearance of morphologically normal myeloid cells and in
all the stages of differentiation, but with a high number of
myelocytes and neutrophils, there are generally basophilia and
thrombocytosis. In the acceleration phase an increase in immature
cells occurs in the peripheral blood and in the blastic crisis the
predominant cell is the myeloblast (65%) or the lymphoblast (35%).
[0032] Vaquez's disease (VD). It is the myeloproliferative syndrome
characterized by the increase in mass of the red series. Vazquez's
disease is a benign haematological disease, whose suffering does
not influence shortening of survival. However, it is a clonal
disease which may evolve in 15% of patients to myelofibrosis or
acute leukemia (5%). [0033] Essential Thrombocythemia (ET).
Myeloproliferative syndrome characterized by platelet production 15
times greater than normal. It may be associated to thrombotic or
hemorrhagic complications secondary to platelet dysfunction. It
appears at around 60 years of age, with equal incidence in both
sexes. [0034] Myelofibrosis (MF). It is a neoplastic clonal
disorder of the pluripotent stem cell. It is characterized by a
great production of abnormal megakaryocytes. These cells release
molecules (growth factor derived from platelets, platelet factor 4)
which stimulate the proliferation of fibroblasts and build collagen
fibres in the bone marrow. The bone marrow is incapable of
functioning normally and the hematopoietic precursor cells
translate to the liver and spleen, giving rise to extramedullary
hematopoiesis. Characterized by fibrosis of B.M and splenomegaly.
It appears in people over 50 years of age and has no preference of
sex.
[0035] Mastocytosis. Group of entities characterized by the
proliferation of mastocytic cells in different parts of the body.
Systemic mastocytosis (SM), is a rare disease which typically
affects adults and has bone alterations in 70% of patients (Chen C
C et al., 1994).
[0036] 1.2. Myelodysplastic/Myeloproliferative Syndromes
(MDS/MPS)
[0037] The WHO has established a somewhat different classification,
separating MDS/MPS as entities differentiated from the other MDS,
since they share characteristics with the CMPS that make them
different. This group includes three entities: chronic
myelomonocytic leukaemia, chronic atypical myeloid, leukeumia,
juvenile myelomonocytic leukaemia and non-classifiable MDS/MPS.
Myelodysplastic syndromes (MDS) are clonal proliferations of the
hematopoeietic stem cell which share at the time of diagnosis,
clinical, morphological and analytical data which are superimposed
between AML and CMPS. They are characterized by the
hypercellularity of bone marrow due to the proliferation of one or
more myeloid lines (Heaney M L, 1999). The presence of dysplasia in
at least one line (myeloid, erythroid or megakaryocytic-platelet)
is a characteristic of MDS. The incidence is variable depending on
the variety. An incidence of 3 cases.times.100,000 inhabitants over
60/year is estimated. The FAB classification establishes 4
diagnostic categories (Bennett J M et al., 1984): simple refractory
anemia (RA), refractory anemia with ring sideroblasts (ARS),
refractory anemia excess blasts (RAEB) and refractory anemia with
excess blasts in transformation (RAEB-T) and chronic myelomonocytic
leukemia (CMML).
[0038] With regard to the MDS, the WHO establishes five
differentiated categories (Harris N L, et al., 1999): refractory
anemia, refractory cytopenia with multiline dysplasia, refractory
anemia with excess blasts, non-classifiable MDS and MDS associated
to an isolated defect in chromosome 5 (of the 5q) or syndrome
5q-.
[0039] 1.3. Acute Myeloblastic Leukemia (AML)
[0040] Clonal proliferation of immature cells of the myeloid line.
They may appear de novo or secondary in patients with
myelodysplastic syndrome (MDS). The classification prepared by the
French-American-British group (FAB) considers eight varieties
(M0-M7) based on morphological criteria and on the immunophenotype
of the neoplastic cells (Bennett J M, et al., 1976). Despite the
fact that this classification has been accepted for many years, the
discovery that many genetic alterations have a predictive
characteristic and the incorporation of the cytogenetic analysis to
the diagnosis of acute leukemias (Bene M C et al., 2001) has made
it possible to subclassify the disease and establish the evaluation
of the prognosis, as occurs with translocation t(15;17) which
characterized promyelocytic variety leukemia which is characterized
by the expression of a retinoic acid receptor (RAR), characteristic
which makes this type of leukaemia sensitive to treatment with
transretinoic acid (TRA) in most cases.
[0041] The WHO classifies AML by incorporating morphological,
immunophenotypical, genetic and clinical data to be able to define
biological homogeneous entities and with clinical relevance. Thus,
AML is classified into four large categories: 1.--AML with
recurrent genetic anomalies. 2.--AML with multiline dysplasia.
3.--AML related to treatment and 4.--non-classifiable AML (ref
WHO). The three first categories recognise the importance of
biological factors which predict the evolution of the process. The
cytogenic analysis represents the most powerful prognosis factor
(Roumier C, et al., 2003). It is used to identify subgroups of AML
with different prognosis: low risk with favourable response to
treatment (t(8;21), t(15;17) or inv(16)), intermediate risk (normal
karyotype or t(9;11) or high risk (inv(3), -5del(5q) or -7del(7q),
or more than three alterations). There is molecular heterogeneity
within the risk group. In some cases of patients with normal
karyotype, the presence of mutations has been found in gene FLT3
(Kottaridis P D, et al., 2001.) and MLL (Dohner K et al.,
2002).
[0042] The medullary image in the microscopic examination of
aspirate is generally that of invasion by cells similar to one
another, of immature morphological characteristics which distort
the normal cell distribution constituting authentic cell sheets.
Medullary hyperproduction conditions which areas of inactive bone
marrow come to again present a new focus of hematopoiesis in the
adult age, in this case of abnormal cells.
[0043] Approximately 80-90% of young patients with AML, achieve
complete remission of the disease after chemotherapy. However, the
majority relapses, and a cure occurs in 30%. The oncogenic
transplant of bone marrow has managed to increase the cure rate to
50%, but it is limited by the availability of identical donor HLA.
It is therefore a group of neoplasias with diverse genetic
abnormalities and variable response to treatment (Giles F J et al.,
2002)
2. Lymphoid Neoplasias
[0044] The WHO's classification is a refinement of the REAL
classification (Harris N L et al. 1994). Three large groups of
lymphoid neoplasias: 1.--Lymphoid neoplasias derived from B cells.
2.--Lymphoid neoplasias derived from T and NK cells. 3.--Hodgkin's
lymphoma. This classification includes solid neoplasias and
lymphoid leukemias, as in many of them their occurs a
transformation from one phase to another and the distinction
between them, may be artificial. Thus, chronic lymphatic leukemia B
and the lymphocytic NHL are originated by the same cell and
represent different manifestations of the same neoplasia, the same
occurs with lymphoblastic lymphoma and lymphoblastic leukemia
[0045] 2.1. Neoplasias Derived from B, T and NK Cells
[0046] The WHO's classification divides these neoplasias in
accordance with the stage of maturity of the cells in neoplasias of
precursor cells and neoplasias of mature cells (WHO Classification
Tumours of Haematopoietic and lymphoid tissues. In Pathology and
genetics of tumours of Haematopoietic and lymphoid tissues. E S
Jaffe, N L Harris, H Stein, J W Vardiman. IARC Press. Lyon, 2001).
Due to the high number of entities described, the following are
highlighted: [0047] Acute lymphoblastic leukemia (ALL): Clonal
proliferation of lymphoid precursors. In approximately 80% of the
cases, the precursors belong to the lymphoid B line. The molecular
analysis of the genetic alterations of the leukemic cells have
significantly contributed to the understanding of the pathogenesis
and prognosis of ALL (Ferrando A A et al., 2005). Despite the fact
that the frequency of genetic subtypes differs in children and in
adults, the general mechanisms which lead to ALL are a consequence
of the abnormal expression of proto-oncogenes due to chromosome
translocations which create fusion genes or a hyperploidy. This
initial oncogenic event is probably insufficient to produce
leukemia and it is believed that other alterations which cooperate
with this first one are necessary to definitively alter the
proliferation and survival of the transformed cell. All these
alterations contribute to the leukemic transformation of the
hematopoietic stem cells or of their progenitors as they affect key
regulating processes, maintaining or increasing their capacity for
self-renewal, escape from the normal proliferation controls,
blocking of differentiation and promoting resistance to apoptotic
signals (Hanahan D, et al., 2000).
[0048] The overall appearance of the bone marrow is similar to that
described for myeloid leukemia. The research of the minimal
residual disease is important, a factor which condiciona with su
presence the probable relapse of the disease. The FAB
classification defines 3 stages in accordance with the morphology
(L1-L3).
[0049] It is the most frequent leukemia in the childhood, and in
the clinical course and the response to treatment depends on the
type of genetic alteration, for example, patients with
hyperdiploidy have a favourable prognosis when it is treated with
treatment schemes which include antimetabolites but, in general
terms, children are cured with standard chemotherapy and
prophylaxis of the CNS and in adults only 20% have prolonged
survival with chemotherapy, the allogenic autologous transplant is
useful for cases considered high risk. [0050] Chronic lymphatic
leukemia (CLL). CLL is characterized by clonal proliferation and
accumulation of lymphocytes with mature appearance and resistant to
apoptosis in B.M, blood and lymphoid organs (Galton D A, 1966).
When the lymphodenopathy is dominant, the clinical symptoms are
called Lymphocytic lymphoma. The lymphocytes affected are line B in
95% of the cases and 5% of the cases involve T lymphocytes.
[0051] It is the most frequent leukemia in the Western world. The
average age of patients diagnosed is 65 years old, only 10-15% of
the cases arise under 50 years (Jemal A et al., 2003). It is the
most common cause of leukaemia in adults of the counties of the
Western world and involves around 25% of all leukemias. The
incidence is 3 cases per each 100,000 inhabitants and year, with a
predominance in males, with a male/female proportion of 1.7:1. In
recent years, it has increasingly been diagnosed in younger
patients. The proportion of cases diagnosed at early stages of the
disease (Rai K R, et al., 1975) has increased from 10 to 50%,
probably due to an early diagnosis thanks to routine lymphocyte
counts. The disease affects more men than women.
[0052] The prognosis and clinical course of the disease is
extremely variable. Some patients have a rapidly progressive
evolution and die in the 2-3 years after the diagnosis, whilst in
others, the course is indolent and they live for 10-20 years
without problems related to the CLL. Intermediate cases occur in
half of patients.
[0053] Approximately, 20% of patients are asymptomatic at the time
of diagnosis, performing this as a consequence of a routine blood
analysis. When symptoms exist, they are not specific and include
fatigue, weakness and discomfort.
[0054] The Binet classification (Binet J L et al., 1981) defines 3
stages of disease in accordance with the concentration of
haemoglobin, number of platelets, number of lymph nodes involved
and the presence of visceromegalies. The Rai classification (Rai K
R et al., 1975) uses the same indicators but classifies patients in
five groups.
[0055] This neoplasia is not characterized by a unique and
recurrent genomic alteration. There are some markers which give a
more unfavourable prognosis such as the presence of deletions in
chromosomes 17 and 11 and those patients with absence of mutations
in IgVh genes (40% of the cases) and high proportion of cells
expressing CD38 is characterized by a more agressive clinical
course and a worse response to treatment (Hamblin T J et al., 1999;
Durig J et al., 2002). Another recently described marker is ZAP-70,
independent prognosis marker whose expression is indirectly related
to the mutational state of the gene of the heavy chains of
immunoglobulins (Crespo M et al., 2003). [0056] Multiple myeloma:
MM). MM is a malignant disease wherein a clone of plasma cells
(terminal cells of the B lymphoid line) of the bone marrow suffers
uncontrolled proliferation. It involves 10-15% of all the malignant
diseases and is characteristic of advanced ages, only 2% of the
cases are diagnosed before 40 years of age. For unknown reasons,
the incidence of the disease is increasing.
[0057] These cells produce and secrete monoclonal immunoglobulin or
fragments of immunoglobulins, composed by a heavy and light chain
class (kappa or lambda). Occasionally, the myeloma cannot be
secreted or the protein is not detectable in serum or urine. The
neoplastic plasma cell produces other molecules such as IL6, tumour
necrosis factor or osteoclast activator factor which contributes to
producing osteolysis, hypercalcemia and renal insufficiency,
characteristics alterations of the disease.
[0058] The diagnosis can be casual on performing an analysis in
patients without symptomology or limited disease (20% of cases).
The disease in these patients can remain stable for years and early
treatment in the asymptomatic phase does not provide any
advantages.
[0059] Patients with monoclonal component but which do not meet the
MM diagnosis are considered carriers of monoclonal gammapathy of
indeterminate meaning (MGIM). Among 10 and 20% of these patients
develop MM in 10 years (Kyle R A, 1997; Zhan F et al., 2002). The
monoclonal component can also be associated to other diseases such
as lymphoma, non-hematological neoplasias and diseases of the
connective tissue. [0060] Lymphoplasmocytoid lymphoma and
Waldenstrom's macroglobulinemia. It is the clinical expression of a
low-degree lymphoproliterative disease, characterized by the
infiltration of anomalous lymphoplasmocytic cells in bone marrow,
lymph node and spleen, accompanied by monoclonal production of
immunoglobin M, which conditions an increase in blood viscosity and
the appearance of haemorrhagic vascular manifestations and by
difficulty in circulation in the small vessels. [0061]
--Non-Hodgkin's lymphoma (NHL). NHL are solid tumours of the
lymphoid tissue which are much more heterogeneous than Hodgkin's
disease. The complexity and diversity of the NHL as regards
morphology, genetics, phenotype and clinical behaviour has given
rise to the existence of multiple classifications, none of them
completely satisfactory.
[0062] It is the most frequent hematological disease and, in terms
of years of life lost, it is the fourth most important neoplasia of
the Western world and it seems that its incidence is
increasing.
[0063] It may appear at all ages, but the average appearance is 50
years of age. The cause of the disease is not clear. Specific
chromosome translocations have been described associated to certain
types of lymphomas, for which reason they are of great use in
diagnosis (Montoto S et al., 2003). Most of the Burkitt-type
lymphomas present translocation t(8;14), wherein the c-MYC oncogene
of chromosome 8 is transferred to the next region in chromosome 14
where the heavy immunoglobins chains are coded. 90% of ollicular
lymphomas are characterized by translocation t(14;18), where the
bcl-2 gene of the chromosome 18 is transferred to the region of the
heavy immunoglobulin chains. It is well known that the
overexpression of bcl-2 inhibits apoptosis (programmed cell death).
It is easy that this chromosome rearranging requires other
stimulation, such as, for example, the coexpression of a second
proto-oncogene or an antigenic stimulation to develop the malignant
proliferation. An example of combination of multiple combined
causes constitute the lymphoma associated to AIDS. The appearance
of aggressive extranodal lymphomas is the result of the combination
of immunosuppression by HIV, deregulation of a proto-oncogene
(c-MYC) and a secondary viral infection (Epstein-Barr's virus), the
same occurs in patients subjected to organ transplant (Harris N L
et al., 2001).
[0064] The clinical presentation of the disease is more irregular
than in Hodgkin's disease. It may behave indolently without
requiring immediate treatment or, in contrast, behave aggressively
which is quickly fatal.
[0065] The most frequent nodal condition is cervical. As regards
extranodal condition, the signs and symptoms depend on the affected
organ. The bone marrow appears infiltrated with greater frequency
in the low degree NHL and may cause pancytopenia. The presence of
malignant cells in peripheral blood is also frequent in low-degree
NHL, but of very bad prognosis in those of high-degree.
[0066] The diagnosis is carried out by the histological study of
the lymphatic tissue. The additional information is obtained by
monoclonal antibodies directed against specific lymphocytic
antigens (immunophenotype); this helps to identify the degree of
maturity of the malignant cell and determine the T or B origin
thereof. The presence of mutation in genes which code Ig in the NHL
of strain B are usually used for the identification of some
subtypes of NHL (Kuppers R et al., 1999).
[0067] 2.2. Hodgkin's Lymphoma (LH)
[0068] It is an infrequent disease and has predilection for the
masculine sex in a proportion of 2/1. It is characterized by the
presence of large cells, bi or multi-nucleus called Reed-Sternberg
(RS) and other smaller and mononuclear cells which appear in a
small quantity in the tumour; the rest of the cells are
lymphocytes, granulocytes, fibroblasts and plasma cells. This
inflammatory infiltrate probably reflects the immune response of
the host with the malignant cells. The nature of the RS and
Hodgkin's cells have been greatly studied but continues being
disputed. They may be derived from an initial stage of the lymphoid
cells.
[0069] In some cases, the existence of DNA for Epstein-Barr's virus
has been detected in the tumour. One hypothesis is that the bimodal
distribution of the disease is due to the infection in young
subjects and the other peak would be caused by average
environmental causes.
[0070] The diagnosis is obtained by biopsy of a lymph node. To plan
the treatment, it is necessary to determine the extension of the
disease. (Kuppers R, 2002; Cossman J, 2001; Devilard E et al.,
2002).
Problems in Classification
[0071] The great quantity of hematopoietic cells and the many
stages of differentiation through which they pass further
complicates the classification of the neoplasis originating from
this type of cells. Despite the efforts to establish a
classification based on "real" entities, some of the categories are
ambiguous and in many cases contain very heterogeneous groups as
regards a response to therapy of clinical course. This
heterogeneity is that responsible for, on the one hand, the
incessant search for markers capable of differentiating some
behaviours from others and, on the other hand, that the disputed
classification of this type of neoplasis is subjected to continuous
revisions.
[0072] An ideal classification system should be precise,
reproducible, easy to use and should especially have biological and
clinical significance (Chan W C, et al., 2005). The current
diagnosis systems and the classification of the hematological
neoplasias are based on the recognition of histological and
morphological, immunophenotypical and cytogenetic characteristics
and study of a molecular marker with prognostic value. However, in
some of the diagnostic categories defined in this way, the
following is observed: [0073] A marked heterogeneous therapy
response. Within the same disease there are patients who reach full
remission, partial remission, do not respond, which relapse after a
certain therapy. The capacity to predict a response is especially
important in this type of neoplasis since the transplant of stem
cells is an effective but toxic alternative response. The capacity
to determine what patients would respond to a conventional therapy
before giving it may be beneficial to be able to apply the most
effective treatment to each patient. [0074] A variable clinical
behaviour. Within this category there are patients whose disease is
going to remain stable for long periods of time and which are not
going to need therapy and those whose disease is going to progress
rapidly requiring aggressive therapy.
[0075] These variations point to the existence of molecular
heterogeneity within the diagnostic categories, differences which
the conventional methods of diagnosis are not capable of
determining and hence, the search for new forms of analysis which
provide a greater resolution in the characterization of this type
of neoplasias.
[0076] In this line, the use of expression arrays have demonstrated
being effective not only in deciphering the biological and clinical
diversity which is found in many tumours, but in understanding the
biological and pathological processes which affect many symptoms
and, in particular, the hematopoietic system. The expression arrays
are ordered arrays of sequences associated to a solid support,
complementary to mRNA or to its corresponding cDNA or cRNA, which
allow the analysis of the differential expression of hundreds or
thousands of genes simultaneously. One of the supports to which
they are frequently bound is to rectangular fragments of glass
similar to slides, a format which is frequently alluded to by the
terms microarray, biochip or, simply, chip. Their use is becoming
increasingly frequent for the diagnosis of various diseases or for
the evolution of the evaluation of the susceptibility of suffering
from them.
First Works of Arrays and Hematological Neoplasias
[0077] In 1999, the Golub group published one of the first articles
referring to the role of arrays in the classification of
hematological neoplasias (Golub T R et al., 1999). An array with
6817 genes represented was used for the study of expression
profiles in AML and ALL. A group of 50 genes was selected with the
capacity of predicting the type of leukemia (class predictor) and
they were used to classify a group of unknown samples in the
correct categories. The study of the expression of these 50 genes
is sufficient for the classification of a sample of acute leukemia
in AML or ALL. Despite the fact that the distinction between AML
and ALL is well established with the current diagnostic methods,
the study revealed the existence of specific expression patterns
associated with each type of acute leukemia and proved the use of
expression profiles in cancer classification.
[0078] In 2000, the Alizadeh group published an article in which a
specialized array is used, the lymphochip which contains genes
expressed preferentially in lymphoid cells or if which an
immunological or oncological importance is known with 17,856
sequences (Alizadeh A A et al., 1999). This group used the
"lymphochip" for the study of gene expression patterns associated
to differences in clinical behaviour in a Diffuse Large B-Cell
Lymphoma (DLCL) (Alizadeh A A, et al. 2000). The DLCL is a NHL with
a very heterogeneous behaviour and impossible to distinguish using
conventional diagnostic methods: 40% of patients respond well to
therapy and have prolonged survival whilst 60% die due to the
disease. The authors found that the gene expression could be
related to the clinical behaviour of the tumours. This was one of
the first articles to speak of arrays for the "subclassification"
of hematological neoplasias, i.e. the use of expression profiles
for the identification of two different groups of DLCL from the
transcriptional standpoint, DLCL subtypes with clinical behaviour
impossible to predict with conventional diagnostic criteria.
[0079] At present there are multiple publications wherein, directly
or indirectly appear the arrays applied not only to classification
and subclassification, but also to the study, diagnosis, prognosis,
identification of new markers in haematological diseases (Greiner
TC, 2004; Alizadeh A A et al, 2000; Bea S et al., 2005; Dave S S et
al., 2004), as well as patent applications which disclose the use
of this type of device for the differentiation between different
types of hematological neoplasias. Thus, for example, patent
application WO2003/008552 discloses the use with diagnostic
purposes of differences in the expression pattern of genes to
differentiate between mixed line leukemia (MLL), acute
lymphoblastic leukemia (ALL) and acute leukemia myelogenous
leukemia (AML), defending the possibility of making this
differential diagnosis with the data obtained after the diagnosis
of samples from patients afflicted by each one of these types of
leukemia by the use of commercial chips from Affymetrix. Although
genes are indicated with variations in the expression between the
three types of leukemias which would permit the differentiation
between them, no specific sequences are mentioned other than those
present in the Affymetrix chip which could have been used to detect
these genes by devices different from those of said company, nor
does it consider the design of devices or methods which would
permit the diagnosis of other types of leukemias or, in general,
neoplasias derived from hematopoietic cells.
[0080] Patent application WO2005/024043, for its part, also relates
to the field of gene expression analysis to go into greater detail
in the knowledge of differences existing at a molecular level
between the different neoplasias derived from hematopoietic cells,
specifically centering on the case of lymphomas, to extract data
which help in its diagnosis or in the prognosis of its evolution.
In particular, it discloses a method to obtain useful functions to
predict the evolution of individuals affected by different types of
lymphomas evaluating in lymph node biopsies to what extent patterns
or genetic prints contribute in each one of them, groups of genes
which are expressed in a coordinated manner and which are related
to the cell origin of the neoplasia, the different types of
non-malignant cells present in the biopsy and the oncogenic
mechanisms responsible for cancer. The different patterns or
genetic prints are also deduced in this case from the data obtained
with commercial chips from Affymetrix. Furthermore, application
WO2005/024043 states it provides an alternative microarray,
composed of a fewer number of sequences than the Affymetrix
microarrays, which would also permit the analysis of differences in
gene expression between lymphomas and their application for
deducing functions of prediction of survival and for the
differentiation between different types of lymphomas. Although it
indicates the genes whose analysis would be made possible by that
microarray, the specification of application WO2005/024043 does not
indicate the sequence of the probes which would compose the
microarray, only mentioning that they would be cDNA type and
leaving doubts over whether that cDNA would appear complete or the
analysis of the corresponding gene expression would be carried out
using as probe only one fragment of said cDNA, which would remain
tp be determined.
[0081] It would be interesting to have compositions and methods
which would permit ifferentiation between neoplasias of
hematopoietic origin based on their molecular level difference,
specifically designed for this group of neoplasias, wherein it
would evaluate the expression of a more reduced number of genes
than in the commercial microarrays used in the studies described in
the aforementioned patient applications and which enabled both the
diagnosis of certain neoplasias and the prediction of their future
evolution, thus helping in the prescription of a suitable treatment
for each patient, a particularly interesting characteristic in
those neoplasias, as is the case of CLL, wherein the prognosis of
the future evolution of the patient is difficult with the knowledge
and tests available to date. Furthermore, it would be particularly
convenient that the probes used to evaluate the expression of the
expressed genes had been designed specifically so that, in addition
to being specific and with a perfectly defined sequence, all had a
similar behaviour, which would make them suitable, in general, to
use in combination in a same test and, in particular, to form part
of the same ordered array associated to a solid support, such as
chips or microarrays. The compositions and methods of this
invention meet this need.
[0082] Instead of commercial microarrays to detect genes
significant for distinguishing between neoplasias or creating
functions which predict the survival of the individual suffering
from it, the invention provides new oligonucleotides, of perfectly
defined sequence, capable of specifically detecting genes which
have been selected as they are known to be significant for the
biology of blood cells or for the pathology of different
neoplasias, oligonucleotides which also have the feature of having
being designed so that they share common characteristics which have
a similar behaviour to those used as probes in hybridization, which
makes them suitable to be used in compositions which comprise
combinations thereof. Said compositions and in particular those
wherein these nucleotides are arranged in ordered form on an easy
to handle solid support such as glass similar to slides, are
suitable for carrying out tests to detect statistically significant
genes or differentiate samples taken from individuals suffering
from certain types of neoplasias originating from hematopoietic
cells of samples taken from individuals not suffering from said
neoplasias, as they are compositions which contain a number of
nucleotides less than those commercial microarrays designed with a
more general purpose, being specifically designed for the analysis
of samples from individuals suffering from neoplasias and composed
of a known sequence of probes, perfectly reproducible, which are
designed to be used together in the same test as they are of
similar behaviour. The additional inclusion in the microarrays of
the invention of oligonucleotides of low homology with human genes,
but chosen so that the rest of their characteristics are similar to
those of the oligonucleotides of the invention designed to act as
probes capable of recognizing human genes with high specificity,
permits the use of said microarrays for the identification of
statistically significant genes in the identification of samples
associated to certain neoplasias of hematopoietic origin by the use
of tests wherein it is feasible to establish controls in all their
phases. As shown in the examples which appear further on, in the
present specification the use of these microarrays in combination
with various statistical techniques permits the correct
classification of different biological samples by a method which is
precise, reproducible, easy to use and with biological and clinical
significance, as they are based on differences of gene expression
with significance for the biological processes which are being
analysed. In particular, the use of a microarray of the invention
in combination with the method of the invention permits the
identification of blood samples in patients suffering from chronic
lymphatic leukemia (alteration not considered in applications
WO2003/008552 and WO2005/024043 and whose diagnosis has not been
described by the use of commercial microarrays), distinguishing
those of both samples obtained from healthy individuals and samples
related to other types of leukemias, and those corresponding to
Jurkat or U937 cells, facilitating the diagnosis of CLL through the
analysis of expression levels of statistically significant genes to
do this and even permitting the obtainment of functions which
enable the mathematical calculation of the probability of a sample
belonging to individuals afflicted with stable chronic lymphatic
leukemia from samples belonging to individuals afflicted with
progressive chronic lymphatic leukemia, a distinction which is now
difficult to carry out a priori by the available techniques, which
means it is a useful and novel tool for the prognosis of the future
evolution of individuals afflicted with this disease, individuals
whose diagnosis may also have been carried out by compositions and
method of the invention or may have been known thanks to the
application of a different method, but for which, on having a tool
which makes it possible to make a prognosis on how the CLL they are
suffering from is going to later evolve, it would be easier to
decide if it is suitable to subject them to an immediate aggressive
treatment or simply keep them under observation to check that their
gene expression data continue indicating that the disease is going
to remain stable for a long period of time.
SUMMARY OF THE INVENTION
[0083] The invention provides compositions which include at least
one oligonucleotide from the group composed of:
SG1, SG2, SG3, SG4, SG5, SG6, SG7, SG8, SG9, SG10, SG11, SG12,
SG13, SG14, SG15, SG16, SG17, SG18, SG19, SG20, SG21, SG22, SG23,
SG24, SG25, SG26, SG27, SG28, SG29, SG30, SG31, SG32, SG33, SG34,
SG35, SG36, SG37, SG38, SG39, SG40, SG41, SG42, SG43, SG44, SG45,
SG46, SG47, SG48, SG49, SG50, SG51, SG52, SG53, SG54, SG55, SG56,
SG57, SG58, SG59, SG60, SG61, SG62, SG63, SG64, SG65, SG66, SG67,
SG68, SG69, SG70, SG71, SG72, SG73, SG74, SG75, SG76, SG77, SG78,
SG79, SG80, SG81, SG82, SG83, SG84, SG85, SG86, SG87, SG88, SG89,
SG90, SG91, SG92, SG93, SG94, SG95, SG96, SG97, SG98, SG99, SG100,
SG101, SG102, SG103, SG104, SG105, SG106, SG107, SG108, SG109,
SG110, SG111, SG112, SG113, SG114, SG115, SG116, SG117, SG118,
SG119, SG120, SG121, SG122, SG123, SG124, SG125, SG126, SG127,
SG128, SG129, SG130, SG131, SG132, SG133, SG134, SG135, SG136,
SG137, SG138, SG139, SG140, SG141, SG142, SG143, SG144, SG145,
SG146, SG147, SG148, SG149, SG150, SG151, SG152, SG153, SG154,
SG155, SG156, SG157, SG158, SG159, SG160, SG161, SG162, SG163,
SG164, SG165, SG166, SG167, SG168, SG169, SG170, SG171, SG172,
SG173, SG174, SG175, SG176, SG177, SG178, SG179, SG180, SG181,
SG182, SG183, SG184, SG185, SG186, SG187, SG188, SG189, SG190,
SG191, SG192, SG193, SG194, SG195, SG196, SG197, SG198, SG199,
SG200, SG201, SG202, SG203, SG204, SG205, SG206, SG207, SG208,
SG209, SG210, SG211, SG212, SG213, SG214, SG215, SG216, SG217,
SG218, SG219, SG220, SG221, SG222, SG223, SG224, SG225, SG226,
SG227, SG228, SG229, SG230, SG231, SG232, SG233, SG234, SG235,
SG236, SG237, SG238, SG239, SG240, SG241, SG242, SG243, SG244,
SG245, SG246, SG247, SG248, SG249, SG250, SG251, SG252, SG253,
SG254, SG255, SG256, SG257, SG258, SG259, SG260, SG261, SG262,
SG263, SG264, SG265, SG266, SG267, SG268, SG269, SG270, SG271,
SG272, SG273, SG274, SG275, SG276, SG277, SG278, SG279, SG280,
SG281, SG282, SG283, SG284, SG285, SG286, SG287, SG288, SG289,
SG290, SG291, SG292, SG293, SG294, SG295, SG296, SG297, SG298,
SG299, SG300, SG301, SG302, SG303, SG304, SG305, SG306, SG307,
SG308, SG309, SG310, SG311, SG312, SG313, SG314, SG315, SG316,
SG317, SG318, SG319, SG320, SG321, SG322, SG323, SG324, SG325,
SG326, SG327, SG328, SG329, SG330, SG331, SG332, SG333, SG334,
SG335, SG336, SG337, SG338, SG339, SG340, SG341, SG342, SG343,
SG344, SG345, SG346, SG347, SG348, SG349, SG350, SG351, SG352,
SG353, SG354, SG355, SG356, SG357, SG358, SG359, SG360, SG361,
SG362, SG363, SG364, SG365, SG366, SG367, SG368, SG369, SG370,
SG371, SG372, SG373, SG374, SG375, SG376, SG377, SG378, SG379,
SG380, SG381, SG382, SG383, SG384, SG385, SG386, SG387, SG388,
SG389, SG390, SG391, SG392, SG393, SG394, SG395, SG396, SG397,
SG398, SG399, SG400, SG401, SG402, SG403, SG404, SG405, SG406,
SG407, SG408, SG409, SG410, SG411, SG412, SG413, SG414, SG415,
SG416, SG417, SG418, SG419, SG420, SG421, SG422, SG423, SG424,
SG425, SG426, SG427, SG428, SG429, SG430, SG431, SG432, SG433,
SG434, SG435, SG436, SG437, SG438, SG439, SG440, SG441, SG442,
SG443, SG444, SG445, SG446, SG447, SG448, SG449, SG450, SG451,
SG452, SG453, SG454, SG455, SG456, SG457, SG458, SG459, SG460,
SG461, SG462, SG465, SG468, SG469, SG470, SG471, SG472, SG473,
SG474, SG475, SG476, SG477, SG478, SG479, SG480, SG481, SG482,
SG483, SG484, SG485, SG486, SG487, SG488, SG489, SG490, SG491,
SG492, SG493, SG494, SG495, SG496, SG497, SG498, SG499, SG500,
SG501, SG502, SG503, SG504, SG505, SG506, SG507, SG508, SG509,
SG510, SG511, SG512, SG513, SG514, SG515, SG516, SG517, SG518,
SG519, SG520, SG521, SG522, SG523, SG524, SG525, SG526, SG527,
SG428, SG529, SG530, SG531, SG532, SG533, SG534, SG535, SG536,
SG537, SG538, SG539, SG540, SG541, SG542, SG543, SG544, SG545,
SG546, SG547, SG548, SG549, SG550, SG551, SG552, SG553, SG554,
SG555, SG556, SG557, SG558, SG559, SG560, SG561, SG562, SG563, or
combinations thereof.
[0084] Said oligonucleotides have been designed so that, in
addition to being specific for the corresponding genes whose
expression one wants to evaluate, they have a similar behaviour, as
they are of similar lengths and all of them have GC in the range of
40% to 60%, in addition to corresponding to zones situated less
than 3000 nucleotides from end 3' (poly(A)) of the mRNA which one
wants to detect and evaluated and of being constituted by sequences
which coincide in their sense with those of the corresponding mRNA.
Therefore, they are suitable to be used in the same test or form
part of a composition which comprises combinations thereof. A
particular embodiment of the invention is constituted by the
compositions which comprise mixtures of several of said
oligonucleotides. Especially preferred are those compositions which
comprise mixtures of oligonucleotides which correspond to genes
significant for classifying a sample as associated to a certain
neoplasia and/or to determine the future evolution thereof.
Especially preferred embodiments of the invention are also those
compositions which comprise the totality of the oligonucleotides
from the group composed of:
SG1, SG2, SG3, SG4, SG5, SG6, SG7, SG8, SG9, SG10, SG11, SG12,
SG13, SG14, SG15, SG16, SG17, SG18, SG19, SG20, SG21, SG22, SG23,
SG24, SG25, SG26, SG27, SG28, SG29, SG30, SG31, SG32, SG33, SG34,
SG35, SG36, SG37, SG38, SG39, SG40, SG41, SG42, SG43, SG44, SG45,
SG46, SG47, SG48, SG49, SG50, SG51, SG52, SG53, SG54, SG55, SG56,
SG57, SG58, SG59, SG60, SG61, SG62, SG63, SG64, SG65, SG66, SG67,
SG68, SG69, SG70, SG71, SG72, SG73, SG74, SG75, SG76, SG77, SG78,
SG79, SG80, SG81, SG82, SG83, SG84, SG85, SG86, SG87, SG88, SG89,
SG90, SG91, SG92, SG93, SG94, SG95, SG96, SG97, SG98, SG99, SG100,
SG101, SG102, SG103, SG104, SG105, SG106, SG107, SG108, SG109,
SG110, SG111, SG112, SG113, SG114, SG115, SG116, SG117, SG118,
SG119, SG120, SG121, SG122, SG123, SG124, SG125, SG126, SG127,
SG128, SG129, SG130, SG131, SG132, SG133, SG134, SG135, SG136,
SG137, SG138, SG139, SG140, SG141, SG142, SG143, SG144, SG145,
SG146, SG147, SG148, SG149, SG150, SG151, SG152, SG153, SG154,
SG155, SG156, SG157, SG158, SG159, SG160, SG161, SG162, SG163,
SG164, SG165, SG166, SG167, SG168, SG169, SG170, SG171, SG172,
SG173, SG174, SG175, SG176, SG177, SG178, SG179, SG180, SG181,
SG182, SG183, SG184, SG185, SG186, SG187, SG188, SG189, SG190,
SG191, SG192, SG193, SG194, SG195, SG196, SG197, SG198, SG199,
SG200, SG201, SG202, SG203, SG204, SG205, SG206, SG207, SG208,
SG209, SG210, SG211, SG212, SG213, SG214, SG215, SG216, SG217,
SG218, SG219, SG220, SG221, SG222, SG223, SG224, SG225, SG226,
SG227, SG228, SG229, SG230, SG231, SG232, SG233, SG234, SG235,
SG236, SG237, SG238, SG239, SG240, SG241, SG242, SG243, SG244,
SG245, SG246, SG247, SG248, SG249, SG250, SG251, SG252, SG253,
SG254, SG255, SG256, SG257, SG258, SG259, SG260, SG261, SG262,
SG263, SG264, SG265, SG266, SG267, SG268, SG269, SG270, SG271,
SG272, SG273, SG274, SG275, SG276, SG277, SG278, SG279, SG280,
SG281, SG282, SG283, SG284, SG285, SG286, SG287, SG288, SG289,
SG290, SG291, SG292, SG293, SG294, SG295, SG296, SG297, SG298,
SG299, SG300, SG301, SG302, SG303, SG304, SG305, SG306, SG307,
SG308, SG309, SG310, SG311, SG312, SG313, SG314, SG315, SG316,
SG317, SG318, SG319, SG320, SG321, SG322, SG323, SG324, SG325,
SG326, SG327, SG328, SG329, SG330, SG331, SG332, SG333, SG334,
SG335, SG336, SG337, SG338, SG339, SG340, SG341, SG342, SG343,
SG344, SG345, SG346, SG347, SG348, SG349, SG350, SG351, SG352,
SG353, SG354, SG355, SG356, SG357, SG358, SG359, SG360, SG361,
SG362, SG363, SG364, SG365, SG366, SG367, SG368, SG369, SG370,
SG371, SG372, SG373, SG374, SG375, SG376, SG377, SG378, SG379,
SG380, SG381, SG382, SG383, SG384, SG385, SG386, SG387, SG388,
SG389, SG390, SG391, SG392, SG393, SG394, SG395, SG396, SG397,
SG398, SG399, SG400, SG401, SG402, SG403, SG404, SG405, SG406,
SG407, SG408, SG409, SG410, SG411, SG412, SG413, SG414, SG415,
SG416, SG417, SG418, SG419, SG420, SG421, SG422, SG423, SG424,
SG425, SG426, SG427, SG428, SG429, SG430, SG431, SG432, SG433,
SG434, SG435, SG436, SG437, SG438, SG439, SG440, SG441, SG442,
SG443, SG444, SG445, SG446, SG447, SG448, SG449, SG450, SG451,
SG452, SG453, SG454, SG455, SG456, SG457, SG458, SG459, SG460,
SG461, SG462, SG465, SG468, SG470, SG472, SG473, SG474, SG475,
SG476, SG477, SG478, SG479, SG480, SG481, SG482, SG483, SG484,
SG485, SG486, SG487, SG488, SG489, SG490, SG491, SG492, SG493,
SG494, SG495, SG496, SG497, SG498, SG499, SG500, SG501, SG502,
SG503, SG504, SG505, SG506, SG507, SG508, SG509, SG510, SG511,
SG512, SG513, SG514, SG515, SG516, SG517, SG518, SG519, SG520,
SG521, SG522, SG523, SG524, SG525, SG526, SG527, SG428, SG529,
SG530, SG531, SG532, SG533, SG534, SG535, SG536, SG537, SG538,
SG539, SG540, SG541, SG542, SG543, SG544, SG545, SG546, SG547,
SG548, SG549, SG550, SG551, SG552, SG553, SG554, SG555, SG556,
SG557, SG558, SG559, SG560, SG561, SG562, SG563.
[0085] Additionally, the invention provides oligonucleotides useful
to be used as controls in the method of the invention. On the one
hand as integrity controls, the pairs of oligonucleotides SG463 and
SG464 (complementary, respectively at ends 5' and 3' of the
.beta.-actin gene) and SG466 and SG467 (complementary,
respectively, to ends 5' and 3' of the GAPD gene) are provided.
Additionally, oligonucleotides SSPC1, SSPC2, SSPC3, SSPC4, SSPC5,
SSPC6 and SSPC7 are provided, which may be used as exogenous
internal positive controls of the process quality after adding to
the sample which contains the starting mRNA molecules of
polyadenylated nucleic acids which contain fragments which
correspond in their sequence to those of these oligonucleotides
(such as the transcripts corresponding to the genes wherefrom said
nucleotides are derived) and which are subjected to the same
processing as the starting mRNA, as well as oligonucleotides SCN2,
SCN3, SCN6, SCN8, SCN11, SCN12 and SCN13, designed to be used as
positive hybridization controls and oligonucleotides SCN1, SCN5,
SCN7, SCN10, SC1, SC2, SC3, SC4, SC5, SC6 and SC7, designed to be
used as negative controls; they all comply with the conditions of
having low homology with human genes, in addition to complying with
the same conditions of the oligonucleotides complementary to human
genes of being of similar lengths and all of them having GC
contents in the range of 40% to 60%, correspond to zones situated
at less than 3000 nucleotides from end 3' (poly(A)) of the
non-human mRNA which would be capable of detecting and being
constituted by sequences which coincide in their sense with those
of the corresponding mRNA. Any composition which contains at least
one of oligonucleotides SG463, SG464, SG466, SG467, SSPC1, SSPC2,
SSPC3, SSPC4, SSPC5, SSPC6, SSPC7, SCN2, SCN3, SCN6, SCN8, SCN11,
SCN12, SCN13, SCN1, SCN5, SCN7, SCN10, SC1, SC2, SC3, SC4, SC5, SC6
and SC7, in combination with at least one of the oligonucleotides
complementary to human genes of the invention mentioned above is
also a composition included in the scope of the present
invention.
[0086] It is especially preferred that the oligonucleotides which
form part of a composition of the invention are bound to a solid
support. In particular, those are preferred of said compositions
wherein the distribution of the oligonucleotides on the solid
support are of ordered form, whereby the solid support is a
rectangular piece of glass similar to a microscope slide and that
the oligonucleotides are bound to the glass by covalent bonds; the
compositions which meet said characteristics are referred to in the
rest of the specification with the words "microarray", "chip" or
"microchip". Among these compositions in the form of microarray,
there is a special preference for those which contain more than one
copy of each one of the oligonucleotides which form part thereof,
very especially preferring that the number of copies of each one of
the nucleotides present is at least 12.
[0087] The scope of the invention also includes any diagnostic
device which comprises a composition of the invention. The
expression "diagnostic device" refers not only to that which serves
to determine if the individual suffers from a disease or not but
also those which serve to classify the disease an individual is
suffering from as belonging to a subtype associated to a determined
form of future evolution of said disease and, which therefore, also
have a prognostic value of the future evolution of the disease.
[0088] The invention also provides a method for diagnosing a
neoplasia originating from hematopoietic cells and/or making a
prognosis of the evolution thereof which comprises the in vitro
detection from a biological sample and the statistical analysis of
the expression level of at least one significant gene for
classifying the sample as associated or not to said neoplasia, a
gene which is selected from the group composed of GABARAP, NPM3,
ABCB1, ABCB4, ABCC3, ABCC5, ABCC6, ABHD1, ABL1, ACTN1, AF1q,
AKR1A1, ALDH1A1, ALK, ANK2, ANPEP, ANXA6, ANXA7, APAF1, APEX,
ARHGEF2, ARS2, ASNS, ATIC, ATM, ATP5O, BAX, BCL10, BCL2, BCL2A1,
BCL2L1, BCL2LAA, BCL3, BCL6, BCL7A, BCL7b, BCR, BECN1, BIK, BIRC3,
BIRC5, BLMH, BLR1, BLVRB, BMI1, BMP6, BRMS1, BST2, BTG1, BUB1,
C21orf33, C5orf13, CA12, CALD1, CANP2, CASC3, CASP1, CASP3, CASP4,
CASP5, CASP6, CASP7, CASP8, CASP9, CAST, CATSD, CBFA2T1, CBFB,
CCNA1, CCNB1, CCND1, CCND2, CCND3, CCNE1, CCR6, CCR7, CCT6A, CD14,
CD19, CD2, CD22, CD24, CD28, CD33, CD34, CD36, CD38, CD3E, CD4,
CD44, CD47, CD48, CD5, CD58, CD59, CD6, CD7, CD79A, CD79B, CD8,
CD81, CD83, CD86, CD9, CDA, CDC25A, CDC25B, CDK2, CDK4, CDK5R1,
CDKN1A, CDKN1B, CDKN1C, CDKN2A, CDKN2B, CDKN2C, CDKN3, CDW52,
CEBPA, CEBPB, CEBPD, CFL1, CKMT1, CKS2, CML66, COL3A1, COL4A6, CR2,
CREB1, CREBBP, CRYAB, CSF2, CSF3, CSRP2, CTGF, CTSB, CUZD1, CXADR,
CXCL9, CXCR3, CXCR4, CYC1, CYP1A1, CYP2A6, DAD-1, DAPK1, DCK, DDX6,
DEK, DHFR, DLAD, DNAJA1, DNMT3B, DNTT, DOK1, DPF2, DPP4, DRG1,
DRP2, E2F1, EB-1, EBI2, EDF1, EEF1A1, EEF1B2, EEF1D, EEF1G, EFNB1,
EGFR, EGR1, EIF2B2, EIF3S2, EIF4B, EIF4E, EIF5A, ELF1, ELF4, ENPP1,
EphA3, EPOR, ERBB2, ERBB4, ERCC1, ERCC2, ERCC3, ERCC5, ERCC6, ETS1,
ETS2, ETV6, ETV7, EZH2, FABP5, FADD, FAIM3, FAM38A, FARP1, FAT,
FCER2, FCGR3A, FCGR3B, FGFR1, FGFR3, FGR, FHIT, FKBP9, FLI1,
FLJ22169, FLT3, FN1, FNTB, FOS, FUS, G1P2, GABPB2, GATA1, GATA2,
GATA3, GCET2, GDI2, GGA3, GJA1, GLUD1, GNL3, GOT1, GRB2, GRIA3,
GRK4, GSTP1, GSTT1, GUSB, GZMA, H2AFX, H3F3A, HCK, HELLS, HIF1A,
HIST1H2BN, HLA-A, HLA-DPA1, HLA-DQA1, HLA-DRA, HLA-DRB3, HLF, HMMR,
HNRPH3, HNRPL, HOXA10, HOXA9, HOXD8, HOXD9, HRAS, HSD17B1, HSPB1,
IBSP, ICAM1, ICAM3, ID2, IER3, IFRD1, IGFBP2, IGFBP3, IGFIR,
IGLV6-57, IL10, IL15, IL1B, IL2, IL2RA, IL3, IL32, IL3RA, IL4R,
IL6, IL6R, IL8, ILF2, IRF1, IRF2, IRF4, IRF8, ITGA2, ITGA3, ITGA4,
ITGA5, ITGA6, ITGAL, ITGAM, ITGAX, ITGB1, ITGB2, JAK1, JAK2, JUNB,
KAI1, KIAA0247, KIAA0864, KIT, KLF1, KLF13, KRAS2, KRT18, LADH,
LAG3, LASP1, LCK, LCP1, LEPR, LGALS3, LGALS7, LIF, LIMS1, LMO2,
LOC285148, LRP, LSP1, LYL1, LYN, LYZ, MAFB, MAFK, MAGEA1, MAL,
MAP3K12, MAP4K1, MAPK10, MAZ, MBP1, MCL1, MCM3, MCM7, MDM2, MEIS1,
MEN1, MERTK, MKI67, MLF1, MLF2, MLL, MLLT10, MME, MMP2, MMP7, MMP8,
MMP9, MNDA, MPL, MPO, MRPL37, MS4A1, MTCP1, MUC-1, MX1, MYB, MYBL1,
MYC, MYOD1, NCALD, NCAM1, NCL, NDP52, NDRG1, NDUFA1, NDUFB, NF1,
NFATC1, NFIC, NFKB1, NFIB1A, NINJ1, NPM1, NR3C1, NUMA1, NXF1, ODC1,
OGGI, OLIG2, OPRD1, p14ARF, P55CDC, PABPC1, PAX5, PAX6, PAX8, PBX1,
PBX3, PCA1, PCD, PCNA, PDCD1, PDGFA, PDGFRB, PDHA1, PGF, PGRMC1,
PICALM, PLA2G6, PLAU, PLK1, PLP, PLS3, PLZF, PML, PMM1, POLR2c,
POU2F2, PPP1CC, PRAME, PRKCI, PRKCQ, PRKDC, PRL, PRTN3, PSMA5,
PSMB4, PSMC5, PSMD7, PTEN, PTGS1, PTHLH, PTK2, PTK2B, PTN, PTPRCCD,
PYGB, RAD51, RAF1, RAG1, RARA, RARB, RB1, RBBP4, RBBP6, RBBP8,
RBP4, RET, RGS1, RGS1, RIS1, RORA, RPL17, RPL23A, RPL24, RPL36A,
RPL37A, RPL41, RPS3, RPS5, RPS9, RUNX1, RxRA, S100A2, S100A8, SDC1,
SDHD, SELE, SELL, SEPW1, SERPINA9, SERPINB5, SERPNINA9, SFTPB,
SIAT4A, SLC7A5, SNRPB, SOSTDC1, SP1, SPI1, SPN, SPRRIA, SREBF1,
SSBP1, STAT1, STAT3, STAT5B, SUMO1, TACSTD2, TAGLN2, TAL1, TBP,
TCEB1, TCF1, TCF3, TCF7, TCL1A, TCRbeta, TEGT, TERF1, TERT, TFCP2,
TFRC, THBS1, THPO, TIA-2, TIAM1, TK1, TLX1, TMEM4, TNF, TNFRSF10C,
TNFRSF1A, TNFRSF25, TNFRSF5, TNFRSF6, TNFRSF8, TNFSF10, TNFSF5,
TNFSF6, TOP2A, TOPORS, TP73, TRA@, TRADD, TRAF3, TRAP1, TRIB2,
TXNRD1, UBE2C, UHRF1, UVRAG, VCAM1, VEGF, VPREB1, WBSCR20C, WNT16,
WTI, XBP1, XPO6, XRCC3, XRCC5, ZAP70, ZFPL1, ZNF42, ZNFN1A1, ZYX,
18S rRNA, 28S rRNA, and whose expression level is determined by the
evaluation of the concentration of its corresponding mRNA by the
use of at least one probe which has a sequence complementary to a
fragment of a strand of said gene, a probe which is selected from
the group of oligonucleotides composed of: SG1, SG2, SG3, SG4, SG5,
SG6, SG7, SG8, SG9, SG10, SG11, SG12, SG13, SG14, SG15, SG16, SG17,
SG18, SG19, SG20, SG21, SG22, SG23, SG24, SG25, SG26, SG27, SG28,
SG29, SG30, SG31, SG32, SG33, SG34, SG35, SG36, SG37, SG38, SG39,
SG40, SG41, SG42, SG43, SG44, SG45, SG46, SG47, SG48, SG49, SG50,
SG51, SG52, SG53, SG54, SG55, SG56, SG57, SG58, SG59, SG60, SG61,
SG62, SG63, SG64, SG65, SG66, SG67, SG68, SG69, SG70, SG71, SG72,
SG73, SG74, SG75, SG76, SG77, SG78, SG79, SG80, SG81, SG82, SG83,
SG84, SG85, SG86, SG87, SG88, SG89, SG90, SG91, SG92, SG93, SG94,
SG95, SG96, SG97, SG98, SG99, SG100, SG101, SG102, SG103, SG104,
SG105, SG106, SG107, SG108, SG109, SG110, SG111, SG112, SG113,
SG114, SG115, SG116, SG117, SG118, SG119, SG120, SG121, SG122,
SG123, SG124, SG125, SG126, SG127, SG128, SG129, SG130, SG131,
SG132, SG133, SG134, SG135, SG136, SG137, SG138, SG139, SG140,
SG141, SG142, SG143, SG144, SG145, SG146, SG147, SG148, SG149,
SG150, SG151, SG152, SG153, SG154, SG155, SG156, SG157, SG158,
SG159, SG160, SG161, SG162, SG163, SG164, SG165, SG166, SG167,
SG168, SG169, SG170, SG171, SG172, SG173, SG174, SG175, SG176,
SG177, SG178, SG179, SG180, SG181, SG182, SG183, SG184, SG185,
SG186, SG187, SG188, SG189, SG190, SG191, SG192, SG193, SG194,
SG195, SG196, SG197, SG198, SG199, SG200, SG201, SG202, SG203,
SG204, SG205, SG206, SG207, SG208, SG209, SG210, SG211, SG212,
SG213, SG214, SG215, SG216, SG217, SG218, SG219, SG220, SG221,
SG222, SG223, SG224, SG225, SG226, SG227, SG228, SG229, SG230,
SG231, SG232, SG233, SG234, SG235, SG236, SG237, SG238, SG239,
SG240, SG241, SG242, SG243, SG244, SG245, SG246, SG247, SG248,
SG249, SG250, SG251, SG252, SG253, SG254, SG255, SG256, SG257,
SG258, SG259, SG260, SG261, SG262, SG263, SG264, SG265, SG266,
SG267, SG268, SG269, SG270, SG271, SG272, SG273, SG274, SG275,
SG276, SG277, SG278, SG279, SG280, SG281, SG282, SG283, SG284,
SG285, SG286, SG287, SG288, SG289, SG290, SG291, SG292, SG293,
SG294, SG295, SG296, SG297, SG298, SG299, SG300, SG301, SG302,
SG303, SG304, SG305, SG306, SG307, SG308, SG309, SG310, SG311,
SG312, SG313, SG314, SG315, SG316, SG317, SG318, SG319, SG320,
SG321, SG322, SG323, SG324, SG325, SG326, SG327, SG328, SG329,
SG330, SG331, SG332, SG333, SG334, SG335, SG336, SG337, SG338,
SG339, SG340, SG341, SG342, SG343, SG344, SG345, SG346, SG347,
SG348, SG349, SG350, SG351, SG352, SG353, SG354, SG355, SG356,
SG357, SG358, SG359, SG360, SG361, SG362, SG363, SG364, SG365,
SG366, SG367, SG368, SG369, SG370, SG371, SG372, SG373, SG374,
SG375, SG376, SG377, SG378, SG379, SG380, SG381, SG382, SG383,
SG384, SG385, SG386, SG387, SG388, SG389, SG390, SG391, SG392,
SG393, SG394, SG395, SG396, SG397, SG398, SG399, SG400, SG401,
SG402, SG403, SG404, SG405, SG406, SG407, SG408, SG409, SG410,
SG411, SG412, SG413, SG414, SG415, SG416, SG417, SG418, SG419,
SG420, SG421, SG422, SG423, SG424, SG425, SG426, SG427, SG428,
SG429, SG430, SG431, SG432, SG433, SG434, SG435, SG436, SG437,
SG438, SG439, SG440, SG441, SG442, SG443, SG444, SG445, SG446,
SG447, SG448, SG449, SG450, SG451, SG452, SG453, SG454, SG455,
SG456, SG457, SG458, SG459, SG460, SG461, SG462, SG465, SG468,
SG469, SG470, SG471, SG472, SG473, SG474, SG475, SG476, SG477,
SG478, SG479, SG480, SG481, SG482, SG483, SG484, SG485, SG486,
SG487, SG488, SG489, SG490, SG491, SG492, SG493, SG494, SG495,
SG496, SG497, SG498, SG499, SG500, SG501, SG502, SG503, SG504,
SG505, SG506, SG507, SG508, SG509, SG510, SG511, SG512, SG513,
SG514, SG515, SG516, SG517, SG518, SG519, SG520, SG521, SG522,
SG523, SG524, SG525, SG526, SG527, SG428, SG529, SG530, SG531,
SG532, SG533, SG534, SG535, SG536, SG537, SG538, SG539, SG540,
SG541, SG542, SG543, SG544, SG545, SG546, SG547, SG548, SG549,
SG550, SG551, SG552, SG553, SG554, SG555, SG556, SG557, SG558,
SG559, SG560, SG561, SG562, SG563.
[0089] The genes which form part of the aforementioned group are
human genes. Therefore, whenever the words "subject" or
"individual" are used hereinafter, they will make reference to a
human being.
[0090] A particular case of this method is that which comprises an
additional previous step of identification of genes significant for
the classification of the biological sample analysed as associated
or not to a specific type of neoplasia originating from
hematopoietic cells, a classification which includes not only the
diagnosis of the existence of said neoplasia in the individual from
which the sample has been taken, but which may also consist, in
additional or alternative form, of the discrimination between
specific subtypes of said neoplasia which correspond to different
future forms of evolution of said neoplasia this constituting the
classification of one or another subtype of the evolution of the
neoplasia considered in the future. In this particular case of the
method of the invention which comprises a previous step of
identification of genes significant for making the desired
classification, said previous step comprises the steps of: [0091]
a) deciding the possible categories wherein the sample can be
classified; [0092] b) obtaining biological samples from individuals
which have previously been assigned by a method different to that
claimed to any of the possible classification categories, so that
there are samples of each one of the possible categories; [0093] c)
obtaining the total mRNA of each one of the samples; [0094] d)
obtaining the corresponding total cRNA, labelled by a method which
allows its subsequent detection, of at least one aliquot of each
one of the samples of mRNA, an aliquot whereto is added before the
obtainment of the cRNA at least one sequence of polyadenylated
nucleotides of low homology with human genes for which it acts as
internal positive control of the process; [0095] e) adding to one
of the aliquots of cRNA which are going to be used in step f) at
least one oligonucleotide of low homology with human genes
different from and not complementary to any possible sequence of
nucleotides which have been added in step d), for which it acts as
positive hybridization control; [0096] f) hybridizing, in strict
conditions, at least one aliquot of total cRNA of each one of the
samples with at least one microarray which comprises at least two
copies of each one of the oligonucleotides from the group composed
of: SG1, SG2, SG3, SG4, SG5, SG6, SG7, SG8, SG9, SG10, SG11, SG12,
SG13, SG14, SG15, SG16, SG17, SG18, SG19, SG20, SG21, SG22, SG23,
SG24, SG25, SG26, SG27, SG28, SG29, SG30, SG31, SG32, SG33, SG34,
SG35, SG36, SG37, SG38, SG39, SG40, SG41, SG42, SG43, SG44, SG45,
SG46, SG47, SG48, SG49, SG50, SG51, SG52, SG53, SG54, SG55, SG56,
SG57, SG58, SG59, SG60, SG61, SG62, SG63, SG64, SG65, SG66, SG67,
SG68, SG69, SG70, SG71, SG72, SG73, SG74, SG75, SG76, SG77, SG78,
SG79, SG80, SG81, SG82, SG83, SG84, SG85, SG86, SG87, SG88, SG89,
SG90, SG91, SG92, SG93, SG94, SG95, SG96, SG97, SG98, SG99, SG100,
SG101, SG102, SG103, SG104, SG105, SG106, SG107, SG108, SG109,
SG110, SG111, SG112, SG113, SG114, SG115, SG116, SG117, SG118,
SG119, SG120, SG121, SG122, SG123, SG124, SG125, SG126, SG127,
SG128, SG129, SG130, SG131, SG132, SG133, SG134, SG135, SG136,
SG137, SG138, SG139, SG140, SG141, SG142, SG143, SG144, SG145,
SG146, SG147, SG148, SG149, SG150, SG151, SG152, SG153, SG154,
SG155, SG156, SG157, SG158, SG159, SG160, SG161, SG162, SG163,
SG164, SG165, SG166, SG167, SG168, SG169, SG170, SG171, SG172,
SG173, SG174, SG175, SG176, SG177, SG178, SG179, SG180, SG181,
SG182, SG183, SG184, SG185, SG186, SG187, SG188, SG189, SG190,
SG191, SG192, SG193, SG194, SG195, SG196, SG197, SG198, SG199,
SG200, SG201, SG202, SG203, SG204, SG205, SG206, SG207, SG208,
SG209, SG210, SG211, SG212, SG213, SG214, SG215, SG216, SG217,
SG218, SG219, SG220, SG221, SG222, SG223, SG224, SG225, SG226,
SG227, SG228, SG229, SG230, SG231, SG232, SG233, SG234, SG235,
SG236, SG237, SG238, SG239, SG240, SG241, SG242, SG243, SG244,
SG245, SG246, SG247, SG248, SG249, SG250, SG251, SG252, SG253,
SG254, SG255, SG256, SG257, SG258, SG259, SG260, SG261, SG262,
SG263, SG264, SG265, SG266, SG267, SG268, SG269, SG270, SG271,
SG272, SG273, SG274, SG275, SG276, SG277, SG278, SG279, SG280,
SG281, SG282, SG283, SG284, SG285, SG286, SG287, SG288, SG289,
SG290, SG291, SG292, SG293, SG294, SG295, SG296, SG297, SG298,
SG299, SG300, SG301, SG302, SG303, SG304, SG305, SG306, SG307,
SG308, SG309, SG310, SG311, SG312, SG313, SG314, SG315, SG316,
SG317, SG318, SG319, SG320, SG321, SG322, SG323, SG324, SG325,
SG326, SG327, SG328, SG329, SG330, SG331, SG332, SG333, SG334,
SG335, SG336, SG337, SG338, SG339, SG340, SG341, SG342, SG343,
SG344, SG345, SG346, SG347, SG348, SG349, SG350, SG351, SG352,
SG353, SG354, SG355, SG356, SG357, SG358, SG359, SG360, SG361,
SG362, SG363, SG364, SG365, SG366, SG367, SG368, SG369, SG370,
SG371, SG372, SG373, SG374, SG375, SG376, SG377, SG378, SG379,
SG380, SG381, SG382, SG383, SG384, SG385, SG386, SG387, SG388,
SG389, SG390, SG391, SG392, SG393, SG394, SG395, SG396, SG397,
SG398, SG399, SG400, SG401, SG402, SG403, SG404, SG405, SG406,
SG407, SG408, SG409, SG410, SG411, SG412, SG413, SG414, SG415,
SG416, SG417, SG418, SG419, SG420, SG421, SG422, SG423, SG424,
SG425, SG426, SG427, SG428, SG429, SG430, SG431, SG432, SG433,
SG434, SG435, SG436, SG437, SG438, SG439, SG440, SG441, SG442,
SG443, SG444, SG445, SG446, SG447, SG448, SG449, SG450, SG451,
SG452, SG453, SG454, SG455, SG456, SG457, SG458, SG459, SG460,
SG461, SG462, SG465, SG468, SG469, SG470, SG471, SG472, SG473,
SG474, SG475, SG476, SG477, SG478, SG479, SG480, SG481, SG482,
SG483, SG484, SG485, SG486, SG487, SG488, SG489, SG490, SG491,
SG492, SG493, SG494, SG495, SG496, SG497, SG498, SG499, SG500,
SG501, SG502, SG503, SG504, SG505, SG506, SG507, SG508, SG509,
SG510, SG511, SG512, SG513, SG514, SG515, SG516, SG517, SG518,
SG519, SG520, SG521, SG522, SG523, SG524, SG525, SG526, SG527,
SG428, SG529, SG530, SG531, SG532, SG533, SG534, SG535, SG536,
SG537, SG538, SG539, SG540, SG541, SG542, SG543, SG544, SG545,
SG546, SG547, SG548, SG549, SG550, SG551, SG552, SG553, SG554,
SG555, SG556, SG557, SG558, SG559, SG560, SG561, SG562, SG563, a
microarray which additionally comprises: [0097] a. at least two
points which correspond to different aliquots of the solvent
wherein nucleotides are found at the time of their deposit on the
surface of the microarray, for which they serve as blank, [0098] b.
at least two copies of at least one oligonucleotide for each one of
the polyadenylated sequences added in step d), an oligonucleotide
whose sequence will correspond to a fragment, different from the
polyadenylation zone, of the sequence of polyadenylated nucleotides
whose evolution in the process has to be controlled; [0099] c. for
each one of the oligonucleotides added in step e), at least two
copies of an oligonucleotide complementary thereto; [0100] d. at
least two copies of each member of at least one pair of
oligonucleotides wherein the sequence of one of the members
corresponds to a sequence of zone 5' and the sequence of the other
corresponds to a sequence of zone 3' of the mRNA of a gene which is
expressed in constitutive form in any cell of hematopoietic origin;
[0101] e. at least two copies of at least one oligonucleotide of
low homology with human genes different from any of the
oligonucleotides defined in section b. and different from any of
the synthetic oligonucleotides added optionally in step e); [0102]
g) detecting and quantifying the signal of cRNA hybridized with
each one of the copies of each one of the oligonucleotides present
in the microarray, as well as the signal corresponding to the
points of the solvent; [0103] h) calculating the average level of
intensity of hybridization of each one of the oligonucleotides of
the microarray calculating the average of the intensities of the
copies of each one of the oligonucleotides; [0104] i) taking the
hybridization as valid if the following conditions are complied
with: [0105] a. the ratio between the average intensity and the
average background of all the oligonucleotides of the microarray is
greater than 10; [0106] b. the value of the average coefficient of
variation of all the replicas of oligonucleotides should be less
than 0.3; [0107] c. the average value of negative control should be
less than 2.5 times the average value of the points corresponding
to the solvent; [0108] d. there is a signal both in the
hybridization controls and in the internal positive controls used
as process control; [0109] j) normalizing the data; [0110] k)
eliminating the oligonucleotides with values of average intensity
minus average background noise less than approximately 2 times the
average value obtained with the points corresponding to the
solvent, as well as the oligonucleotides with an interquartile
range of normalized intensity throughout the samples less than 0.3;
[0111] l) performing the statistical analysis to find the
statistically significant oligonucleotides to differentiate between
the different categories and be able to classify a sample which has
not been previously assigned to any category, choosing said
oligonucleotides among those which have not been eliminated in the
previous steps, until obtaining "n" oligonucleotides which either
have a value of p less than a limit which is chosen from the open
range of 0 to 0.05, preferably using for it a method with capacity
to reduce false positives, or that which best defines the category
established; [0112] m) checking that the grouping of the samples
according to the differences in intensities between the different
samples detected for the statistically significant oligonucleotides
gives rise to the samples being classified in the same categories
as those which had previously been assigned by a different
method.
[0113] It is preferred that the average value calculated in section
h) is the trimmed mean, for which reason it is preferable that the
microarray comprises at least four copies of each one of the
oligonucleotides present therein.
[0114] The normalization can be carried out with different methods.
There is preference for the use of functions contained in access
packages freely accessed over the Internet designed for the
processing, calculation and graphic representation of data, such as
the packages designed in R programming language, available to
download from CRAN (http://cran.r-project.org/) or Bioconductor
(http://www.bioconductor.orq). The "variance stabilization
normalization" method available in the "vsn" package in R.
[0115] The identification of the statistically significant
oligonucleotides to differentiate between the different categories
can be carried out using different methods, having preference for
those wherein a value p is determined that determines the threshold
of probability under which all the genes whose expression
difference has a value less than p would be considered significant
and, among these, those which have the capacity to carry out
corrections on the value of p, such as, among others, Bonferroni's
method or Welch's test. The value of p will be chosen from the open
range of 0 to 0.05, preferring, when possible, a value of p close
to 0.001 and with correction, it being possible to increase said
value at maximum to 0.05 (value which is not included among those
possible) until which statistically significant oligonucleotides
are found to differentiate between the categories among which one
wants to classify the samples. A possibility for carrying out these
calculations is, again, the use of functions contained in packages
freely accessed over the Internet designed for the processing,
calculation and graphic representation of data. In particular, the
mt.maxT function of the multtest package in R can be used for the
identification of the statistically significant
oligonucleotides.
[0116] Another possibility for the identification of statistically
significant oligonucleotides to be able to differentiate between
the categories of established samples is the use of the "nearest
shrunken centroids" method, a variation of the "nearest centroids"
method (Tibshirani et al., 2002), which identifies a group of genes
which best characterizes a predefined class and uses this group of
genes to predict the class which new samples belong to. To do this,
again functions contained in packages freely accessed over the
internet may be resorted to, such as the "pam.sup.a" package in R,
wherein it is possible to find functions to carry out the so-called
"Prediction Analysis for Microarrays (PAM)", which makes use of the
"nearest shrunken centroids" method.
[0117] After identifying the statistically significant genes to
distinguish between categories of samples established from the
corresponding oligonucleotides, they can be used for classifying
new samples due to similarity between the expression profile of
those genes in the sample analysed and those corresponding to each
one of the classification categories. Alternatively, when there are
only 2 possible classification categories (which will be normal
when one wants to diagnose the presence or absence of a certain
type of leukaemia in an individual), it is possible to obtain a
mathematical function of classification of samples which determine
the probability "p.sub.i" of a sample "i" belonging to one category
or another. To do this, a subunit of the samples is chosen which
have been previously assigned to each one of the possible
categories by a method different to that of the invention and the
value of 0 is arbitrarily associated to each one of the samples of
one of the categories "a" (typically, the category of "not"
associated to the leukemia one wants to diagnose") of belonging to
the other possible category, whilst each one of the samples of the
subunit belonging to the other possible category "b" (typically,
the category of "associated" to the leukemia one wants to
diagnose") arbitrarily receives the value "1" for its probability
of belonging to its own category. With this, logistical regression
is used to calculate, with the aid of the probability values
assigned to each one of the samples and the values of normalized
trimmed mean intensity obtained for each one of the samples with
each one of the "n" oligonucleotides which has been identified as a
statistically significant oligonucleotide in the previous step,
coefficients for each one of said oligonucleotides which make it
possible to obtain a function of probability p.sub.i of a sample
"i" belonging to category "b", a function which will be of the
type
p.sub.i=1/(1+e.sup.-xi)
and which results from the algebraic transformation of the
expression which equals Neperian logarithm of the quotient between
the probability of an event occurring and the probability that it
does not occur at a function x.sub.i which includes as variables
each one of the factors which may influence the event, i.e.
ln p 1 - p = x i ##EQU00001##
function x.sub.i which, in the present case, will depend on the
intensity values obtained for each one of the statistically
significant oligonucleotides and which responds to an expression of
the type:
x i = constant + m = 1 n ( coeff_olig m * lmn i _olig m )
##EQU00002##
where [0118] coeff_olig.sub.m represents the coefficient calculated
for a specific oligonucleotide "m" [0119]
Imn.sub.i.sub.--olig.sub.m represents the average value of
normalized intensity obtained in the hybridization of the sample i
calculated for the oligonucleotide "m" [0120] "m" varies from 1 to
"n" [0121] n is the total number of oligonucleotides considered
significant.
[0122] The function p.sub.i obtained after calculating by
logistical regression the coefficient corresponding to each
oligonucleotide permits classifying a sample "i" as belonging to
one or another category, considering that the values of p.sub.i
over 0.5 (and which will be less than or equal to 0) indicate that
the sample belongs to category "b", whilst the values of p.sub.i
less than 0.5 indicate that the sample belongs to category "a".
Said function p.sub.i will be considered valid if, on being applied
to the samples wherefrom it has been deduced, it is capable of
classifying them correctly and, furthermore, as it is applied to
the subgroup of samples which have not been taken into account to
deduce the function, but whose category is known as it has been
previously assigned by a method other than that of the invention,
it is also capable of classifying them correctly.
[0123] Alternatively, when the identification of the statistically
significant genes has been performed using the "Prediction Analysis
for Microarrays" method, the classifier can be obtained with the
corresponding functions of the "pamr.sup.a" package in R, which
also starts from the assignment of the value of probability 0 to a
subgroup of members of one of the categories and the value of
probability 1 to a subgroup of the members of the other category.
Again, the calculation of coefficients for statistically
significant oligonucleotides permits the calculation of values of
probability of belonging to one or another category, also
considering that the values over 0.5 indicate belonging to the
category whose members are arbitrarily assigned value 1 and the
values less than 0.5 indicate belonging to the other category.
[0124] A particular case of the method of the invention is that
wherein one wants to classify samples as associated or not to a
type of leukemia. In that case, blood samples are preferred,
especially those of peripheral blood, as biological samples to
carry out in vitro the method of the invention.
[0125] Once the statistically significant genes have been
identified to associate a determined type of neoplasia as
originating from hematopoietic cells, the method of the invention
can be used for classifying samples according to the expression
level of said genes in said samples. The neoplasia can be, for
example, a specific type of leukemia. A particular case of this
embodiment of the method of the invention is constituted by the
association of chronic lymphatic leukemia, thus allowing the
diagnosis of this disease by the method of the invention. To do
this, significant genes are considered to be those genes whose
expression level is analysed on applying the method of the
invention at least those of the group of CD79A, FAIM3, HLA-DRA,
HLA-DRB3, HLA-DQA1 and the analysis is carried out on blood
samples. The method can be additionally applied including the
analysis of the expression level of at least genes IRF8 and COL3A1.
Preferably, the analysis of the expression level of these genes is
carried out by evaluating the level of their corresponding mRNA by
hybridization of their corresponding cRNA with oligonucleotides
SG117, SG428, SG459, SG507, SG508, SG461 and SG493, which are
preferred to be associated to a solid support forming part of a
microarray. When the evaluation of the hybridized cRNA with each
one of those oligonucleotides is carried out thanks to the prior
labelling of the cRNA with biotin, the staining of the microarray
hybridized with streptavidin conjugated with a fluorophore and the
detection of the signal emitted by said fluorophore, it is
preferred that the fluorophore is Cy3, which permits diagnosing the
presence of CLL in the subject from which the sample has been taken
by the classification of sample "i" analysed as associated to CLL
from the calculation of the probability that said sample is
associated to CLL from the formula p.sub.i=1/(1+e.sup.-x.sup.i),
wherein x.sub.i is calculated by the formula
x.sub.i=-719.241486+(2.44756372*Imn.sub.i.sub.--CD79A)+(7.38657611*Imn.s-
ub.i.sub.--FAIM3)+(23.1465464*Imn.sub.i.sub.--HLA-DRA)+(43.6287742*Imn.sub-
.i.sub.--IRF8)-(19.3978182*Imn.sub.i.sub.--COL3A1)-(2.80282646*Imn.sub.i.s-
ub.--HLA-DRB3)+(49.5345672*Imn.sub.i.sub.--HLA-DQA1) [0126] formula
wherein each one of the values denominated with the abbreviation
"Imn.sub.i" followed by the abbreviation of a gene makes reference
to the average value of normalized intensity obtained after
detecting the hybridization signal corresponding to the
oligonucleotide which is being used as probe to evaluate the
expression of the said gene and which permits classifying the
subject as subject not suffering from CLL if the value of p.sub.i
is less than 0.5 and as subject suffering from CLL if the value of
p.sub.i is greater than 0.5. Alternatively, significant genes can
be considered as those whose expression level is analysed on
applying the method of the invention for the diagnosis of CLL at
least those of the group of CD79A, FAIM3, HLA-DRA, HLA-DRB3,
HLA-DQA1, additionally including the analysis of the expression
level of at least gene CDW52. Preferably, the analysis of the
expression level of these genes is carried out by evaluating the
level of its corresponding mRNA by hybridization of its
corresponding cRNA with oligonucleotides SG117, SG428, SG459,
SG507, SG508 and SG237, which it is preferred are associated to a
solid support forming part of a microarray.
[0127] Another particular case of the application of the method of
the invention for classifying samples as associated to a specific
type of leukemia according to the expression level in said samples
of statistically significant genes constitutes the classification
of a sample as associated to a specific subtype of chronic
lymphatic leukemia, "stable" CLL or "progressive" CLL, which makes
it possible that the method of the invention serves to make a
prognosis for the future evolution of subjects which have been
diagnosed with CLL. When the samples analysed are of peripheral
blood, the genes considered statistically significant to perform
the classification of the samples are at least genes PSMB4, FCER2
and POU2F2, it being possible to additionally analyse the
expression level of at least one gene selecting the group composed
of ODC1, CD79A, CD2, CD3E, CD5, MS4A1, EIF4E, FHIT, NR3C1, LCP1,
MAPK10, ABCC5, XRCC3, CML66, PLZF, RBP4 or the totality
thereof.
[0128] An additional aspect of the invention is the use of devices
to evaluate the expression level of at least one of the genes of
the group composed of PSMB4, FCER2, POU2F2, ODC1, CD79A, CD2, CD3E,
CD5, MS4A1, EIF4E, FHIT, NR3C1, LCP1, MAPK10, ABCC5, XRCC3, CML66,
PLZF, RBP4, CD79A, FAIM3, HLA-DRA, HLA-DRB3, HLA-DQA1, IRF8 and
COL3A1 with the aim of diagnosing the presence of CLL in an
individual and/or making a prognosis of his/her evolution. A
particular case of this aspect of the invention is the use of
devices of evaluation of the expression level of at least one gene
of the group composed of CD79A, FAIM3, HLA-DRA, HLA-DRB3, HLA-DQA1,
IRF8 and COL3A1 for the diagnosis of the presence of CLL in an
individual, wherein it is preferred that the device evaluates at
least the expression level of genes CD79A, FAIM3, HLA-DRA,
HLA-DRB3, HLA-DQA1, it being possible for the device to evaluate,
additionally, the expression level of at least genes IRF8 and
COL3A1 or at least gene CDW52. Another particular case of this
aspect of the invention is the use of devices of evaluation of the
expression level of at least one gene of the group composed of
PSMB4, FCER2, POU2F2, ODC1, CD79A, CD2, CD3E, CD5, MS4A1, EIF4E,
FHIT, NR3C1, LCP1, MAPK10, ABCC5, XRCC3, CML66, PLZF, RBP4, CD79A,
FAIM3, HLA-DRA, HLA-DRB3, HLA-DQA1, IRF8 and COL3A1 to make a
prognosis of the future evolution of CLL in an individual.
DETAILED DESCRIPTION OF THE INVENTION
Design of the Microarray Device
Genes Included in the Microarray
[0129] A revision was performed of the scientific literature and
genes were selected due to their special involvement in the biology
of blood cells or in the pathology of the different neoplasias The
genes selected can be included within these 4 large groups:
a) With an Important Role in the Biology of the Hematopoietic
Cells:
[0130] Genes whose protein is expressed or repressed in the
different steps through which these cells pass in their
differentiation to mature forms. [0131] Genes whose protein is
specifically expressed in accordance with the line whereto the cell
belongs. [0132] Genes which code adhesion molecules
b) Involved in Different Types of Hematological Neoplasias:
[0132] [0133] Genes whose expression (a level of mRNA or protein)
is altered in different types of neoplasias, or associated to
resistance to chemotherapy
c) Cancer-Related:
[0133] [0134] Genes which code proteins associated with
proliferation, metastasis or genes whose expression is increased in
a large number of tumours.
d) Described in Publications Related to Neoplasias:
[0134] [0135] Genes which, without having a special ratio with
hematological neoplasias or blood cell biology, have appeared in
the scientific literature as statistically associated to a type of
neoplasia
[0136] The characteristics of the genes can be consulted, for
example, in: www.ncbi.nlm.nih.qov/Genbank, selecting the "Gene"
option in the drop-down menu which appears and entering the
corresponding identification number (GenID) in the GenBank. The
genes whose expression can be analysed with the microarray, their
corresponding identification number in the GenBank, as well as the
oligonucleotides present in the microarray to be used as probes to
analyse the expression of said genes appear below in Table 1.
Probes of Oligonucleotides which Represent Each Gene.
[0137] For each one of the 534 genes related to hematological
neoplasias, as well as for the genes corresponding to .beta.-actin,
glyceraldehyde-3-phosphate dehydrogenase, 18S rRNA and 28S rRNA,
the mrRNA sequence is sought in GenBank
(www.ncbi.hlm.nih.gov/Genbank/). An oligonucleotide is designed
(probe) from the GenBank sequence, specific for each one of the
genes selected. In some genes several oligonucleotides were
designed situated in zones 5' and 3' of the gene, in order to
analyse the integrity of the mRNA.
[0138] To ensure specificity in the design of the probes, the
following criteria were taken into consideration: [0139] Length of
the probe to guarantee that all the probes are going to have a
similar behaviour, [0140] GC content of the probe between 40 and
60%. This characteristic is also taken into consideration to ensure
that all the probes are going to have a similar behaviour. [0141]
Localization in the gene. Probes localized at least 3000
nucleotides from 3' (poly(A)) of the selected mRNA sequence were
localized. [0142] Sense of the probe. A strand was chosen with
"sense", i.e. the sequences of the oligonucleotides coincide with
sequences of fragments of the corresponding mRNA, instead of being
sequences complementary to said fragments. This decision involves
that the labelled genetic material has to be antisense
(complementary to sense). [0143] Specificity of the probe. To avoid
non-specific hybridization, probes were selected which have a
percentage of homology, calculated by the BLAST tool (available on
the website http://www.ncbi.nlm.nih.gov/), less than 70%.
[0144] The data on the oligonucleotides used as probes, the
identification number of its corresponding sequence in the attached
list, as well as data (identification number in GenBank, usual
abbreviation and name) of the genes for the detection of whose
expression said oligonucleotides have been designed, are shown
below in the Table 1.
TABLE-US-00001 TABLE 1 Oligonucleotides used as probes to detect
the expression of human genes Oligo- Usual nucleotide SEQ ID NO:
GenID abbreviation Description SG1 SEQ ID 11337 GABARAP Protein
associated to the GABA receptor NO: 1 SG2 SEQ ID 28778 IGLV6-57
Variable lambda immunoglobulin 6-57 NO: 2 SG3 SEQ ID 5092 PCD
6-pyruvoyl-tetrahydropterine NO: 3 synthase/dimerization cofactor
of the nuclear factor of 1 alpha hepatocytes (TCF1) SG4 SEQ ID
83988 NCALD delta neurocalcin NO: 4 SG5 SEQ ID 58511 DLAD
deoxyribonuclease II beta NO: 5 SG6 SEQ ID 25928 SOSTDC1 which
contains a sclerostin 1 domain NO: 6 SG7 SEQ ID 10630 TIA-2
glycoprotein associated to the lung cell NO: 7 membrane, type I SG8
SEQ ID 5834 PYGB phosphorylase, glycogen; brain NO: 8 SG9 SEQ ID
3987 LIMS1 with domains LIM and similar to the antigen NO: 9 of
senescent cells 1 SG10 SEQ ID 25 ABL1 homologue to the viral
oncogene of Abelson NO: 10 v-abl 1 murine leukemia SG11 SEQ ID 4733
DRG1 GTP-binding protein regulated by NO: 11 development 1 SG12 SEQ
ID 25855 BRMS1 Metastasis suppressor of breast cancer 1 NO: 12 SG13
SEQ ID 84696 ABHD1 which contains an abhydrolase 1 domain NO: 13
SG14 SEQ ID 3475 IFRD1 Development regulator related to interferon
1 NO: 14 SG15 SEQ ID 6173 RPL36A Ribosomal protein L36a NO: 15 SG16
SEQ ID 3485 IGFBP2 Binding protein to the growth factor similar NO:
16 to insulin 2, 36 kDa SG17 SEQ ID 10397 NDRG1 Gene regulated
downstream by N-myc 1 NO: 17 SG18 SEQ ID 11328 FKBP9 FK506
9-binding protein, 63 kDa NO: 18 SG19 SEQ ID 10241 NDP52 protein of
the nuclear domain 10 NO: 19 SG20 SEQ ID 2171 FABP5 protein which
binds to fatty acids 5 NO: 20 (associated to psoriasis) SG21 SEQ ID
10160 FARP1 protein with FERM, RhoGEF (ARHGEF) NO: 21 and
pleckstrin 1 domains (derived from chrondrocytes) SG22 SEQ ID 5228
PGF Placental growth factor, protein related to NO: 22 the
endothelial growth factor SG23 SEQ ID 2665 GDI2 GDP 2 dissociation
inhibitor NO: 23 SG24 SEQ ID 8407 TAGLN2 transgelin 2 NO: 24 SG25
SEQ ID 645 BLVRB biliverdin reductase B (flavin reductase NO: 25
(NADPH)) SG26 SEQ ID 5692 PSMB4 subunit of proteasome (prosome, NO:
26 macropain), beta-type, 4 SG27 SEQ ID 4070 TACSTD2 transducer of
the calcium signal associated NO: 27 to tumours 2 SG28 SEQ ID 6921
TCEB1 Elongation factor of transcription B (SIII), NO: 28
polypeptide 1 (15 kDa, elongin C) SG29 SEQ ID 1915 EEF1A1
elongation factor in the eukaryotic NO: 29 translation 1 alpha 1
SG30 SEQ ID 3020 H3F3A histone H3, family 3A NO: 30 SG31 SEQ ID
4953 ODC1 ornithine decarboxylase 1 NO: 31 SG32 SEQ ID 7520 XRCC5
Of repair of X rays which complement the NO: 32 defective repair in
Chinese hamster cells 5 (reconnection of breakages in the double
helix; autoantigen Ku, 80 kDa) SG33 SEQ ID 3486 IGFBP3 binding
protein to growth factor similar to NO: 33 insulin 3 SG34 SEQ ID
4691 NCL nucleolin NO: 34 SG35 SEQ ID 6273 S100A2 calcium S100
A2-binding protein NO: 35 SG36 SEQ ID 6152 RPL24 ribosomal protein
L24 NO: 36 SG37 SEQ ID 2697 GJA1 Bone filling protein, alpha 1, 43
kDa NO: 37 (connexin 43) SG38 SEQ ID 2990 GUSB glucuronidase, beta
NO: 38 SG39 SEQ ID 3292 HSD17B1 hydroxysteroid (17-beta)
dehydrogenase 1 NO: 39 SG40 SEQ ID 6439 SFTPB surfactant protein,
associated to lung B NO: 40 SG41 SEQ ID 6147 RPL23A ribosomal
protein L23a NO: 41 SG42 SEQ ID 1466 CSRP2 protein rich in cysteine
and glycine 2 NO: 42 SG43 SEQ ID 1525 CXADR receptor of the
coxsackie virus and NO: 43 adenovirus SG44 SEQ ID 1937 EEF1G
elongation factor of eukartyotic 1 gamma NO: 44 elongation SG45 SEQ
ID 1164 CKS2 subunit regulating the kinase CDC28 2 NO: 45 protein
SG46 SEQ ID 1288 COL4A6 collagen, type IV, alpha 6 NO: 46 SG47 SEQ
ID 1410 CRYAB crystalline, alpha B NO: 47 SG48 SEQ ID 1537 CYC1
cytochrome c-1 NO: 48 SG49 SEQ ID 2342 FNTB farnesyltransferase,
CAAX box, beta NO: 49 SG50 SEQ ID 2805 GOT1 glutamic-oxaloacetic
transaminase 1, NO: 50 soluble (aminotransferase 1 aspartate) SG51
SEQ ID 3963 LGALS7 Lectin, which binds to galactosides, soluble,
NO: 51 7 (galectin 7) SG52 SEQ ID 5268 SERPINB5 Serine (or
cysteine) inhibitor proteinase, NO: 52 clade B (ovalbumin, member 5
SG53 SEQ ID 5705 PSMC5 Subunit of proteasome (prosome, NO: 53
macropain) 26S, ATPase, 5 SG54 SEQ ID 5764 PTN pleiotrophin (growth
factor of bonding to NO: 54 heparin 8, growth promoter factor of
neurites 1) SG55 SEQ ID 5932 RBBP8 Retinoblastoma 8-binding protein
NO: 55 SG56 SEQ ID 5996 RGS1 Regulator of the signalling by
proteins G 1 NO: 56 SG57 SEQ ID 6256 RXRA Retinoid X receptor,
alpha NO: 57 SG58 SEQ ID 6392 SDHD succinate dehydrogenase complex,
subunit NO: 58 D, integral membrane protein SG59 SEQ ID 6415 SEPW1
selenoprotein W, 1 NO: 59 SG60 SEQ ID 6742 SSBP1 binding protein to
single-strand DNA 1 NO: 60 SG61 SEQ ID 7009 TEGT transcript of gene
increased in the testicle NO: 61 (BAX 1 inhibitor) SG62 SEQ ID 8341
HIST1H2BN histone 1, H2bn NO: 62 SG63 SEQ ID 8678 BECN1 beclin 1
(protein similar to myosin which NO: 63 interacts with BCL2, of
twisted helix) SG64 SEQ ID 310 ANXA7 annexin A7 NO: 64 SG65 SEQ ID
4694 NDUFA1 Alpha subcomplex of NADH NO: 65 dehydrogenase
(ubiquinone) 1, 1, SG66 SEQ ID 9181 ARHGEF2 guanine rho/rac
exchange factor (GEF) 2 NO: 66 SG67 SEQ ID 9315 C5orfl3 Open
reading frame 13 of chromosome 5 NO: 67 SG68 SEQ ID 7494 XBP1 X 1
box-binding protein NO: 68 SG69 SEQ ID 9636 G1P2 protein inducible
by the alpha interferon NO: 69 (clone IFI-15K) SG70 SEQ ID 2746
GLUD1 glutamate dehydrogenase 1 NO: 70 SG71 SEQ ID 6273 S100A2
calcium S100 A2-binding protein NO: 71 SG72 SEQ ID 3927 LASP1 LIM
and SH3 1 protein NO: 72 SG73 SEQ ID 10630 TIA-2 glycoprotein
associated to the lung cell NO: 73 membrane type I SG74 SEQ ID
10857 PGRMC1 Membrane component of the progesterone NO: 74 1
receptor SG75 SEQ ID 7542 ZFPL1 protein similar to that of zinc
finger 1 NO: 75 SG76 SEQ ID 11184 MAP4K1 Kinase protein activated
by mitogens 1 NO: 76 SG77 SEQ ID 6772 STAT1 Signal transducer and
transcription activator NO: 77 1, 91 kDa SG78 SEQ ID 3189 HNRPH3
Heterogeneous nuclear ribonucleoprotein NO: 78 H3 (2H9) SG79 SEQ ID
10330 TMEM4 Transmembrane protein 4 NO: 79 SG80 SEQ ID 9766
KIAA0247 KIAA0247 NO: 80 SG81 SEQ ID 25907 RIS1 of senescence
induced by Ras 1 NO: 81 SG82 SEQ ID 51593 ARS2 Arsenate-resistant
protein ARS2 NO: 82 SG83 SEQ ID 771 CA12 Carbonic anhydrase XII NO:
83 SG84 SEQ ID 1933 EEF1B2 elongation factor of the eukaryotic 1
beta 2 NO: 84 translation SG85 SEQ ID 28951 TRIB2 homologue to
tribbles 2 (Drosophila) NO: 85 SG86 SEQ ID 79065 FLJ22169 similar
to that of autophagy 9 APG9 1 (S. cerevisiae) NO: 86 SG87 SEQ ID
440 ASNS asparagine synthetase NO: 87 SG88 SEQ ID 260294 WBSCR20C
Chromosome region 20C of Williams NO: 88 Beuren syndrome SG89 SEQ
ID 10327 AKR1A1 member A1 of the aldo-keto reductase 1 NO: 89
family (aldehyde reductase) SG90 SEQ ID 6698 SPRR1A Small proline
1A-rich protein NO: 90 SG91 SEQ ID 1947 EFNB1 ephrin-B1 NO: 91 SG92
SEQ ID 6193 RPS5 ribosomal protein S5 NO: 92 SG93 SEQ ID 6203 RPS9
ribosomal protein S9 NO: 93 SG94 SEQ ID 6139 RPL17 ribosomal
protein L17 NO: 94 SG95 SEQ ID 2114 ETS2 homologue to oncogene E26
of the NO: 95 erythroblastosis virus v-ets 2 (avian) SG96 SEQ ID
1975 EIF4B initiation factor of the eukaryotic translation NO: 96
4B SG97 SEQ ID 7791 ZYX Zyxin NO: 97 SG98 SEQ ID 23214 XPO6
exportin 6 NO: 98 SG99 SEQ ID 285148 LOC285148 Hypothetical protein
LOC285148 NO: 99 SG100 SEQ ID 8209 C21orf33 open reading frame 33
of chromosome 21 NO: 100 SG101 SEQ ID 1936 EEF1D elongation factor
of the eukaryotic NO: 101 translation 1 delta (guanine nucleotide
exchange protein) SG102 SEQ ID 26986 PABPC1 poly(A)-binding
protein, cytoplasmic 1 NO: 102 SG103 SEQ ID 5930 RBBP6
retinoblastoma 6-binding protein NO: 103 SG104 SEQ ID 3265 HRAS
homologue to the viral oncogene of the NO: 104 Harvey v-Ha-ras rat
sarcoma SG105 SEQ ID 23163 GGA3 ARF-binding protein, which contains
NO: 105 gamma-adaptin, associated to golgi SG106 SEQ ID 1072 CFL1
cophilin 1 (non-muscular) NO: 106 SG107 SEQ ID 8668 EIF3S2
initiation factor of the eukaryotic translation NO: 107 3, subunit
2 beta, 36 kDa SG108 SEQ ID 3875 KRT18 keratine 18 NO: 108 SG109
SEQ ID 3480 IGFIR growth factor receptor similar to insulin 1 NO:
109 SG110 SEQ ID 3576 IL8 Interleukin 8 NO: 110 SG111 SEQ ID 3659
IRF1 Interferon regulating factor 1 NO: 111 SG112 SEQ ID 3660 IRF2
Interferon regulating factor 2 NO: 112 SG113 SEQ ID 4067 LYN
Homologue to the oncogene related to the NO: 113 viral sarcoma of
Yamaguchi V-yes-1 SG114 SEQ ID 4069 LYZ Lysozyme (renal
amiloidosis) NO: 114 SG115 SEQ ID 4792 NFKB1A Nuclear factor of the
gene enhancer of the NO: 115 kappa light polypeptide in B
L-lymphocytes (p105) SG116 SEQ ID 4150 MAZ Zinc finger protein
associated to MYC NO: 116 (transcription factor of binding to
purins) SG117 SEQ ID 973 CD79A Antigen CD79A (associated to alpha
NO: 117 immunoglobulins) SG118 SEQ ID 4172 MCM3 Deficient
maintenance of minichromosomes
NO: 118 (S. cerevisiae) 3 SG119 SEQ ID 421 MEIS1 Homologue to Meis1
(mouse) NO: 119 SG120 SEQ ID 5657 PRTN3 Proteinase 3 (serine
proteinase, NO: 120 autoantigen of Wegener's granulomatosis of
neutrophils) SG121 SEQ ID 4313 MMP2 Metalloproteinase of matrix 2
(gelatinase A, NO: 121 72 kD gelatinase of, 72 kD collagenase type
IV) SG122 SEQ ID 4316 MMP7 Metalloproteinase of matrix 7
(matrilysin, NO: 122 uterine) SG123 SEQ ID 4317 MMP8
Metalloproteinase of matrix 8 (neutrophil NO: 123 collagenase)
SG124 SEQ ID 1796 DOK1 Adapter protein 1, 62 kD (downstream NO: 124
respect to thyrosine kinase 1) SG125 SEQ ID 5154 PDGFA Alpha
polypeptide of the platelet-derived NO: 125 growth factor SG126 SEQ
ID 5617 PRL Prolactin NO: 126 SG127 SEQ ID 5894 RAF1 Homologue to
the viral oncogene of murine NO: 127 leukemia V-raf-1 1 SG128 SEQ
ID 5915 RARB Retinoic acid receptor, beta NO: 128 SG129 SEQ ID 4985
OPRD1 Opioid receptor, delta 1 NO: 129 SG130 SEQ ID 5979 RET
proto-oncogene ret (multiple endocrine NO: 130 neoplasia and
medullary thyroid carcinoma 1, Hirschsprung's disease) SG131 SEQ ID
6720 SREBF1 Transcription factor of binding to sterol NO: 131
regulatory elements 1 SG132 SEQ ID 7124 TNF Tumour necrosing factor
(TNF superfamily, NO: 132 member 2) SG133 SEQ ID 7013 TERF1 Binding
factor to telomeric repetitions NO: 133 (which interact with NIMA)
1 SG134 SEQ ID 7412 VCAM1 Molecule of adhesion to vascular cells 1
NO: 134 SG135 SEQ ID 539 ATP5O ATP synthase, H+ carrier,
mitochondrial F1 NO: 135 complex, subunit O (protein which gives
sensitivity to oligomycin) SG136 SEQ ID 959 TNFSF5 Tumour necrosing
factor (ligand) NO: 136 superfamily, member 5 (hyper-IgM syndrome)
SG137 SEQ ID 5432 POLR2C Polypeptide C (directed at DNA) of the RNA
NO: 137 polymerase II (33 kD) SG138 SEQ ID 8398 PLA2G6
Phospholipase A2, group VI (cytosolic, NO: 138 calcium-dependent)
SG139 SEQ ID 908 CCT6A TCP1 which contains chaperonin, subunit NO:
139 6A (zeta 1) SG140 SEQ ID 5160 PDHA1 Pyruvate dehydrogenase
(lipoamide) alpha 1 NO: 140 SG141 SEQ ID 3939 LADH Lactate
dehydrogenase A NO: 141 SG142 SEQ ID 6628 SNRPB Polypeptides B and
B1 of the small nuclear NO: 142 ribonucleoprotein SG143 SEQ ID 6628
SNRPB Polypeptides B and B1 of the small nuclear NO: 143
ribonucleoprotein SG144 SEQ ID 3014 H2AFX Histone family H2A,
member X NO: 144 SG145 SEQ ID 51253 MRPL37 Mitochondrial ribosomal
protein L37 NO: 145 SG146 SEQ ID 11065 UBE2C Enzyme which
conjugates with ubiquin E2C NO: 146 SG147 SEQ ID 6188 RPS3
Ribosomal protein S3A NO: 147 SG148 SEQ ID 216 ALDH1A1 Aldehyde
dehydrogenase 1 family, member NO: 148 A1 SG149 SEQ ID 10962 AF1q
Lymphoid/myeloid or leukemia or of mixed NO: 149 line (homologue to
trithorax, Drosophila); translocated to 11 SG150 SEQ ID 861 RUNX1
Runt 1-related transcription (acute myeloid NO: 150 leukemia 1;
oncogene aml1) SG151 SEQ ID 4603 MYBL1 Similar to the homologue of
the viral NO: 151 oncogene of avian myeloblastisis V-myb 1 SG152
SEQ ID 309 ANXA6 Annexin A6 NO: 152 SG153 SEQ ID 238 ALK Anaplastic
lymphoma kinase (Ki-1) NO: 153 SG154 SEQ ID 4332 MNDA Antigen for
nuclear differentiation myeloid NO: 154 cells SG155 SEQ ID 317
APAF1 Apoptotic protease activator factor NO: 155 SG156 SEQ ID 330
BIRC3 which contains IAP repetitions of NO: 156 baculovirus 3 SG157
SEQ ID 368 ABCC6 ATP-binding module, subfamily C NO: 157
(CFTR/MRP), member 6 SG158 SEQ ID 471 ATIC
5-aminoimidazol-4-carboxamide NO: 158 ribonucleotide
formyltransferase/IMP cyclohydrolase SG159 SEQ ID 472 ATM Mutated
ataxia-telangiectasia (includes NO: 159 complementary groups A, C
and D) SG160 SEQ ID 581 BAX protein X associated to BCL2 NO: 160
SG161 SEQ ID 595 CCND1 Cyclin D1 (PRAD1: parathyroidal NO: 161
adenomatosis 1) SG162 SEQ ID 596 BCL2 CLL/lymphoma of B 2
lymphocytes NO: 162 SG163 SEQ ID 602 BCL3 CLL/lymphoma of B 3
lymphocytes NO: 163 SG164 SEQ ID 604 BCL6 CLL/lymphoma of B 6
lymphocytes (protein NO: 164 with zinc fingers 51) SG165 SEQ ID 605
BCL7A CLL/lymphoma of B 7A lymphocytes NO: 165 SG166 SEQ ID 9275
BCL7b CLL/lymphoma of B 7B lymphocytes NO: 166 SG167 SEQ ID 8915
BCL10 CLL/lymphoma of B 10 lymphocytes NO: 167 SG168 SEQ ID 598
BCL2L1 similar to BCL2 1 NO: 168 SG169 SEQ ID 613 BCR Grouping
breaking point region NO: 169 SG170 SEQ ID 613 BCR Grouping
breaking point region NO: 170 SG171 SEQ ID 10215 OLIG2
Transcription factor of oligodendrocytes 2 NO: 171 line SG172 SEQ
ID 638 BIK Mortal factor which interacts with BCL2 NO: 172
(apoptosis inducer) SG173 SEQ ID 10018 BCL2LAA Similar to BCL2
(which facilitates NO: 173 apoptosis) SG174 SEQ ID 648 BMI1
Homologue to the viral oncogene of murine NO: 174 leukemia (bmi-1)
SG175 SEQ ID 642 BLMH bleomycin hydrolase NO: 175 SG176 SEQ ID 643
BLR1 Burkitt 1 lymphoma receptor, GTP-binding NO: 176 protein SG177
SEQ ID 3381 IBSP Integrin-binding sialoprotein (bone NO: 177
sialoprotein bone sialoprotein II) SG178 SEQ ID 694 BTG1 Gene of
translocation of B lymphocytes, NO: 178 anti-proliferative SG179
SEQ ID 699 BUB1 Disinhibited budding by benzimidazoles 1 NO: 179
(homologue of yeasts) SG180 SEQ ID 25 ABL1 homologue to the viral
oncogene of that of NO: 180 Abelson's murine leukemia v-abl 1 SG181
SEQ ID 834 CASP1 caspase 1, apoptosis-related cysteine NO: 181
protease (interleukin 1, beta, convertase) SG182 SEQ ID 836 CASP3
caspase 3, apoptosis-related cysteine NO: 182 protease SG183 SEQ ID
837 CASP4 caspase 4, apoptosis-related cysteine NO: 183 protease
SG184 SEQ ID 838 CASP5 caspase 5, apoptosis-related cysteine NO:
184 protease SG185 SEQ ID 839 CASP6 caspase 6, apoptosis-related
cysteine NO: 185 protease SG186 SEQ ID 840 CASP7 caspase 7,
apoptosis-related cysteine NO: 186 protease SG187 SEQ ID 841 CASP8
caspase 8, apoptosis-related cysteine NO: 187 protease SG188 SEQ ID
842 CASP9 caspase 9, apoptosis-related cysteine NO: 188 protease
SG189 SEQ ID 865 CBFB Nucleus binding factor, beta subunit NO: 189
SG190 SEQ ID 800 CALD1 Caldesmon 1 NO: 190 SG191 SEQ ID 831 CAST
Calpastatin NO: 191 SG192 SEQ ID 993 CDC25A Cell division cycle 25A
NO: 192 SG193 SEQ ID 994 CDC25B Cell division cycle 25B NO: 193
SG194 SEQ ID 914 CD2 Antigen CD2 (p50), sheep red blood cell NO:
194 receptor SG195 SEQ ID 916 CD3E Antigen CD3E, epilson
polypeptide NO: 195 (complex TiT3) SG196 SEQ ID 920 CD4 Antigen CD4
(p55) NO: 196 SG197 SEQ ID 921 CD5 Antigen CD5 (p56-62) NO: 197
SG198 SEQ ID 923 CD6 Antigen CD6 NO: 198 SG199 SEQ ID 924 CD7
Antigen CD7 (p41) NO: 199 SG200 SEQ ID 925 CD8 Antigen CD8, alpha
polypeptide(p32) NO: 200 SG201 SEQ ID 928 CD9 Antigen CD9 (p24) NO:
201 SG202 SEQ ID 4311 MME Membrane metalloendopeptidase (neutral
NO: 202 endopeptidase, encephalinase, CALLA, CD10) SG203 SEQ ID
3683 ITGAL Integrin, alpha L (antigen CD11A (p180), NO: 203 antigen
associated to the function of lymphocytes 1; alpha polypeptide)
SG204 SEQ ID 3684 ITGAM Integrin, alpha M (complement 3 NO: 204
component receptor, alpha; also known as CD11b (p170), polypeptide
of the macrophage alpha antigen) SG205 SEQ ID 3687 ITGAX Integrin,
alpha X (antigen CD11C (p150), NO: 205 alpha polypeptide) SG206 SEQ
ID 90 ANPEP Alanyl-(membrane)aminopeptidase NO: 206 (aminopeptidase
N, aminopeptidase M, microsomal aminopeptidase, CD13, p150) SG207
SEQ ID 929 CD14 Antigen CD14 NO: 207 SG208 SEQ ID 6401 SELE
Selectin E (endothelial adhesion molecule NO: 208 1) SG209 SEQ ID
2214 FCGR3A Low-affinity receptor IIIa for the Fc fragment NO: 209
of IgG (CD16) SG210 SEQ ID 2215 FCGR3B Low-affinity receptor IIIb
for the Fc fragment NO: 210 of IgG (CD16) SG211 SEQ ID 3689 ITGB2
Integrin, beta 2 (antigen CD18 (p95), NO: 211 antigen associated to
the function of the lymphocytes 1; beta subunit of the microphage 1
(mac-1) antigen) SG212 SEQ ID 930 CD19 Antigen CD19 NO: 212 SG213
SEQ ID 931 MS4A1 Of 4 domains which are expanded by the NO: 213
membrane, subfamily A, member 1 SG214 SEQ ID 1380 CR2 Complement
component receptor NO: 214 (3d/Epstein Barr's virus) 2 SG215 SEQ ID
933 CD22 Antigen CD22 NO: 215 SG216 SEQ ID 2208 FCER2 Low-affinity
receptor II for the Fc fragment NO: 216 of IgE (CD23A) SG217 SEQ ID
934 CD24 Antigen CD24 (antigen of carcinoma of NO: 217 small lung
cells of the grouping 4) SG218 SEQ ID 3559 IL2RA interleukin 2
receptor, alpha NO: 218 SG219 SEQ ID 1803 DPP4 Dipeptidyl peptidase
IV (CD26, protein NO: 219 which forms complexes with adenosine
deaminase 2) SG220 SEQ ID 3688 ITGB1 Integrin, beta 1 (fibronectin
receptor, beta NO: 220 polypeptide, antigen CD29 includes MDF2,
MSK12) SG221 SEQ ID 943 TNFRSF8 Tumour necrosing factor receptor
NO: 221 superfamily, member 8 SG222 SEQ ID 945 CD33 Antigen CD33
(gp67) NO: 222 SG223 SEQ ID 947 CD34 Antigen CD34 NO: 223 SG224 SEQ
ID 948 CD36 Antigen CD36 (collagen type I receptor, NO: 224
thrombospondin receptor) SG225 SEQ ID 952 CD38 Antigen CD38 (p45)
NO: 225 SG226 SEQ ID 958 TNFRSF5 Tumour necrosing factor receptor
NO: 226 superfamily, member 5 SG227 SEQ ID 6693 SPN Sarcospan (Gene
associated to the Kras NO: 227 oncogene) SG228 SEQ ID 960 CD44
Antigen CD44 (homing function and Indian NO: 228 blood group
function) SG229 SEQ ID 960 CD44v6 Antigen CD44 (homing function and
Indian NO: 229 blood group function) SG230 SEQ ID 5788 PTPRCCD
Protein thyrosine phosphatase, receptor NO: 230 type, C SG231 SEQ
ID 961 CD47 Antigen CD47 (Antigen related to Rh, NO: 231 transducer
of the signal associated to integrins) SG232 SEQ ID 3673 ITGA2
Integrin, alpha 2 (CD49B, alpha 2 subunit of NO: 232 receptor
VLA-2) SG233 SEQ ID 3675 ITGA3 Integrin, alpha 3 (Antigen CD49C,
alpha NO: 233 subunit 3 of receptor VLA-3) SG234 SEQ ID 3676 ITGA4
Integrin, alpha 4 (Antigen CD49D, alpha NO: 234 subunit 4 of
receptor VLA-4) SG235 SEQ ID 3678 ITGA5 Integrin, alpha 5
(fibronectin receptor, alpha
NO: 235 polypeptide) SG236 SEQ ID 3385 ICAM3 Intercellular adhesion
molecule 3 NO: 236 SG237 SEQ ID 1043 CDW52 Antigen CDW52 (antigen
CAMPATH-1) NO: 237 SG238 SEQ ID 3383 ICAM1 Intercellular adhesion
molecule 1 (CD54), NO: 238 human rhinovirus receptor SG239 SEQ ID
4684 NCAM1 Neural cell adhesion molecule 1 NO: 239 SG240 SEQ ID 965
CD58 Antigen CD58 (antigen associated to the NO: 240 function of
the lymphocytes 3) SG241 SEQ ID 966 CD59 Antigen CD59 p18-20
(antigen identified by NO: 241 the monoclonal antibodies 16.3A5,
EJ16, EJ30, EL32 and G344) SG242 SEQ ID 6402 SELL Selectin L
(lymphocyte adhesion molecule NO: 242 1) SG243 SEQ ID 974 CD79B
Antigen CD79B (associated to beta NO: 243 immunoglobulins) SG244
SEQ ID 975 CD81 Antigen CD81 (target of the antiproliferative NO:
244 antibody 1) SG245 SEQ ID 3732 KAI1 Kangai 1 (suppression of
tumorigenicity 6, NO: 245 prostate; antigen CD82 (leukocytes R2
antigen, antigen detected by the monoclonal antibody IA4)) SG246
SEQ ID 9308 CD83 Antigen CD83 (activated B lymphocytes, NO: 246
immunoglobulins superfamily) SG247 SEQ ID 942 CD86 Antigen CD86
(ligand 2 of the antigen NO: 247 CD28, antigen B7-2) SG248 SEQ ID
355 TNFRSF6 Tumour necrosing factor receptor NO: 248 superfamily,
member 6 SG249 SEQ ID 356 TNFSF6 Tumour necrosing factor receptor
NO: 249 superfamily (ligand), member 6 SG250 SEQ ID 8140 SLC7A5
Solute-carrier family 7 (cationic amino acid NO: 250 carrier, y+
system), member 5 SG251 SEQ ID 6382 SDC1 Sindecan 1 NO: 251 SG252
SEQ ID 1019 CDK4 Cyclin-dependent kinase 4 NO: 252 SG253 SEQ ID
6774 STAT3 Signal transducer and transcription activator NO: 253 3
(response factor in acute phase) SG254 SEQ ID 2268 FGR Homologue to
Gardner-Rasheed's feline NO: 254 viral sarcoma oncogene(v-fgr)
SG255 SEQ ID 2353 FOS Homologue to the murine viral NO: 255
osteosarcoma oncogene V-fos FBJ SG256 SEQ ID 898 CCNE1 Cyclin E1
NO: 256 SG257 SEQ ID 978 CDA Cytidine deaminase NO: 257 SG258 SEQ
ID 9935 MAFB Homologue to the fibrosarcoma NO: 258 oncogene (avian)
musculoaponeurotic V- maf SG259 SEQ ID 4352 MPL Oncogene of
myeloproliferative leukemia NO: 259 virus SG260 SEQ ID 4609 MYC
Homologue to the avian myelocyomatosis NO: 260 viral oncogene V-myc
SG261 SEQ ID 4602 MYB Homologue to the avian myelocyomatosis NO:
261 viral oncogene V-myb SG262 SEQ ID 1159 CKMT1 Creatine kinase,
mitochondrial 1 (ubicuous) NO: 262 SG263 SEQ ID 1387 CREBBP CREB
binding protein (Rubinstein-Taybi's NO: 263 syndrome) SG264 SEQ ID
1490 CTGF Connective tissue growth factor NO: 264 SG265 SEQ ID 2833
CXCR3 Chemokene receptor 3 (motive C--X--C) NO: 265 SG266 SEQ ID
7852 CXCR4 Chemokene receptor 4 (motive C--X--C) NO: 266 (fusin)
SG267 SEQ ID 8900 CCNA1 Cyclin A1 NO: 267 SG268 SEQ ID 891 CCNB1
Cyclin B1 NO: 268 SG269 SEQ ID 894 CCND2 Cyclin D2 NO: 269 SG270
SEQ ID 1543 CYP1A1 Cytochrome P450, subfamily I (inducible by NO:
270 aromatic compounds), polypeptide 1 SG271 SEQ ID 1565 CYP2A6
Cytochrome P450, subfamily IID (of NO: 271 metabolization of
debrisokine, spartin, etc.), polypeptide 6 SG272 SEQ ID 1603 DAD-1
Defender against cell death 1 NO: 272 SG273 SEQ ID 8794 TNFRSF10C
Tumour necrosing factor receptor NO: 273 superfamily, member 10c,
decoy without intracellular domain SG274 SEQ ID 7913 DEK Oncogene
DEK (which binds to DNA) NO: 274 SG275 SEQ ID 1633 DCK
Deoxycytidine kinase NO: 275 SG276 SEQ ID 1719 DHFR Dihydrofolate
reductase NO: 276 SG277 SEQ ID 6929 TCF3 Transcription factor 3
(immunoglobulin NO: 277 enhancer binding factors E2A E12/E47) SG278
SEQ ID 1869 E2F1 Transcription factor E2F 1 NO: 278 SG279 SEQ ID
6929 TCF3 Transcription factor 3 (immunoglobulin NO: 279 enhancer
binding factors E2A E12/E47) SG280 SEQ ID 56899 EB-1 Protein
associated to E2a-Pbx1 NO: 280 SG281 SEQ ID 1236 CCR7 Chemokene
receptor 7 (motive C-C) NO: 281 SG282 SEQ ID 1880 EBI2 Gene induced
by Epstein-Barr's 2 disease NO: 282 (receptor coupled to G proteins
specific for lymphocytes) SG283 SEQ ID 4582 MUC-1 Mucin 1,
transmembrane NO: 283 SG284 SEQ ID 2042 EphA3 EPHA3 NO: 284 SG285
SEQ ID 2057 EPOR Erythropoietin receptor NO: 285 SG286 SEQ ID 2067
ERCC1 Of repair of excision which NO: 286 intercomplements the
deficiency in the repair of rodents, complementation group 1
(includes the antisense overlapping sequence) SG287 SEQ ID 2068
ERCC2 Of repair of excision which NO: 287 intercomplements the
deficiency in the repair of rodents, complementation group 2
(xerodermia pigmentoso 2) SG288 SEQ ID 2071 ERCC3 Of repair of
excision which NO: 288 intercomplements the deficiency in the
repair of rodents, complementation group 3 (complements group B of
xerodermia pigmentoso) SG289 SEQ ID 2073 ERCC5 Of repair of
excision which NO: 289 intercomplements the deficiency in the
repair of rodents, complementation group 5 (xerodermia pigmentoso,
complementation group G (Cockayne's syndrome)) SG290 SEQ ID 2074
ERCC6 Of repair of excision which NO: 290 intercomplements the
deficiency in the repair of rodents, complementation group 6 SG291
SEQ ID 50624 CUZD1 With CUB domains and similar to the zone NO: 291
pellucida 1 SG292 SEQ ID 2120 ETV6 Gene variant of ets 6 (TEL
oncogene) NO: 292 SG293 SEQ ID 1977 EIF4E Initiation factor of
eukaryotic translation 4E NO: 293 SG294 SEQ ID 1984 EIF5A
Initiation factor of eukaryotic translation 5A NO: 294 SG295 SEQ ID
2146 EZH2 Zeste homologue enhancer (Drosophila) 2 NO: 295 SG296 SEQ
ID 8772 FADD Associated to Fas (TNFRSF6) via NO: 296 apoptopic
domain SG297 SEQ ID 5747 PTK2 Thyrosine kinase 2 protein NO: 297
SG298 SEQ ID 2195 FAT Homologue to the FAT tumour suppressor NO:
298 (Drosophila) SG299 SEQ ID 2260 FGFR1 Fibroblast growth factor
receptor 1 NO: 299 (thyrosine kinase related to fms 2, Pfeiffer's
syndrome) SG300 SEQ ID 2261 FGFR3 Fibroblast growth factor receptor
3 NO: 300 (achondroplasia, thanatophoric dwarfism) SG301 SEQ ID
2272 FHIT Fragile histidine triad gene NO: 301 SG302 SEQ ID 2322
FLT3 Thyrosine kinase related to Fms 3 NO: 302 SG303 SEQ ID 2892
GRIA3 Glutamate receptor, ionotrophic, AMPA 3 NO: 303 SG304 SEQ ID
2521 FUS Fusion, derived from the malignant NO: 304 liposarcoma
t(12;16) SG305 SEQ ID 1977 EIF4E Initiation factor of eukaryotic
translation 4E NO: 305 SG306 SEQ ID 6482 SIAT4A Sialyltransferase
4A (beta-galactosidase NO: 306 alpha-2.3-Sialyltransferase) SG307
SEQ ID 1440 CSF3 Colony stimulating factor 3 (granulocyte) NO: 307
SG308 SEQ ID 1437 CSF2 Colony stimulating factor 2 (granulocyte-
NO: 308 microphage) SG309 SEQ ID 2908 NR3C1 Subfamily of nuclear
receptors 3, group C, NO: 309 member 1 SG310 SEQ ID 2952 GSTT1
Glutathion S-transferase theta 1 NO: 310 SG311 SEQ ID 3001 GZMA
Granzime A (granzime 1, serine stearase NO: 311 associated to
cytotoxic T lymphocytes 3) SG312 SEQ ID 3301 DNAJA1 Homologue to
DnaJ (Hsp40), subfamily A, NO: 312 member 1 SG313 SEQ ID 3131 HLF
Hepatic leukemia factor NO: 313 SG314 SEQ ID 684 BST2 Antigen of
bone marrow stroma cells 2 NO: 314 SG315 SEQ ID 3205 HOXA9 Homeotic
box A9 NO: 315 SG316 SEQ ID 3195 TLX1 T lymphocyte leukemia,
homeotic box 1 NO: 316 SG317 SEQ ID 29128 UHRF1 similar to
ubiquitine, which contains PHD NO: 317 domains and RING fingers, 1
SG318 SEQ ID 8870 IER3 Immediate early response 3 NO: 318 SG319 SEQ
ID 3553 IL1B Interleukin 1, beta NO: 319 SG320 SEQ ID 3558 IL2
Interleukin 2 NO: 320 SG321 SEQ ID 3562 IL3 Interleukin 3 (multiple
colony stimulating NO: 321 factor) SG322 SEQ ID 3569 IL6
Interleukin 6 (interferon, beta 2) NO: 322 SG323 SEQ ID 3570 IL6R
Interleukin receptor 6 NO: 323 SG324 SEQ ID 3586 IL10 Interleukin
10 NO: 324 SG325 SEQ ID 3600 IL15 Interleukin 15 NO: 325 SG326 SEQ
ID 3662 IRF4 Interferon regulating factor 4 NO: 326 SG327 SEQ ID
3716 JAK1 Janus 2 kinase (a thyrosine kinase protein) NO: 327 SG328
SEQ ID 3717 JAK2 Janus 1 kinase (a thyrosine kinase protein) NO:
328 SG329 SEQ ID 4288 MKI67 Antigen identified by monoclonal
antibody NO: 329 Ki-67 SG330 SEQ ID 7520 XRCC5 Of repair of X rays
which complements the NO: 330 defective repair in Chinese hamster
cells 5 (reconnection of breakages in the double helix; autoantigen
Ku, 80 kDa) SG331 SEQ ID 3902 LAG3 Lymphocyte activation gene 3 NO:
331 SG332 SEQ ID 3932 LCK Lymphocyte specific protein thyrosine NO:
332 kinase SG333 SEQ ID 3936 LCP1 Cytosolic protein of lymphocytes
1 (L- NO: 333 plastin) SG334 SEQ ID 3953 LEPR Leptin receptor NO:
334 SG335 SEQ ID 4005 LMO2 With LIM domains only 2 (similar to NO:
335 rombotin 1) SG336 SEQ ID 3976 LIF Leukemia inhibiting factor
(cholinergic NO: 336 differentiation factor) SG337 SEQ ID 9961 LRP
Main leap protein NO: 337 SG338 SEQ ID 4046 LSP1
Lymphocyte-specific protein 1 NO: 338 SG339 SEQ ID 4066 LYL1
Sequence derived from lymphoblastic NO: 339 leukemia 1 SG340 SEQ ID
4790 NFKB1 Nuclear factor of the enhancer of the gene NO: 340 of
the light kappa polypeptide in B-1 lymphocytes(p105) SG341 SEQ ID
4118 MAL mal, T lymphocyte differentiation protein NO: 341 SG342
SEQ ID 4100 MAGEA1 Melanoma antigen, family A, 1 (directs the NO:
342 expression of antigen MZ2-E) SG343 SEQ ID 5602 MAPK10 Protein
kinase activated by mitogens 10 NO: 343 SG344 SEQ ID 2023 MBP1
Enolase 1, (alpha) NO: 344 SG345 SEQ ID 4170 MCL1 Leukemia sequence
of myeloid cells 1 NO: 345 (related to BCL2) SG346 SEQ ID 4193 MDM2
Human homologue of the double mouse NO: 346 diminuta 2; p53-binding
protein SG347 SEQ ID 5243 ABCB1 ATP binding module, subfamily B NO:
347 (MDR/TAP), member 1 SG348 SEQ ID 5244 ABCB4 ATP binding module,
subfamily B NO: 348 (MDR/TAP), member 4 SG349 SEQ ID 4221 MEN1
Multiple endocrine neoplasia I
NO: 349 SG350 SEQ ID 4283 CXCL9 Chemokene ligand 9 (motive C--X--C)
NO: 350 SG351 SEQ ID 4291 MLF1 Myeloid leukemia factor 1 NO: 351
SG352 SEQ ID 4297 MLL Myeloid/lymphoid leukemia or of mixed line
NO: 352 (homologue to trithorax (Drosophila)) SG353 SEQ ID 4318
MMP9 Metalloproteinase of matrix 9 (gelatinase B, NO: 353 92 kD
gelatinase, 92 kD collagenase type IV) SG354 SEQ ID 4707 NDUFB NADH
dehydrogenase (ubiquinone) 1 beta NO: 354 subcomplex, 1 (7 kD,
MNLL) SG355 SEQ ID 4353 MPO Myeloperoxidase NO: 355 SG356 SEQ ID
8714 ABCC3 ATP binding module, subfamily C NO: 356 (CFTR/MRP),
member 3 SG357 SEQ ID 10057 ABCC5 ATP binding module, subfamily C
NO: 357 (CFTR/MRP), member 5 SG358 SEQ ID 4515 MTCP1 Proliferation
of mature T-lymphocytes 1 NO: 358 SG359 SEQ ID 4515 MTCP1
Proliferation of mature T-lymphocytes 1 NO: 359 SG360 SEQ ID 4654
MYOD1 Myogenic factor 3 NO: 360 SG361 SEQ ID 4599 MX1 Resistance to
Myxovirus (flu) 1, homologue NO: 361 to the murine protein (protein
inducible by interferon p78) SG362 SEQ ID 4814 NINJ1 Ninjurin 1 NO:
362 SG363 SEQ ID 4869 NPM1 Nucleophosmin (nucleolar phosphoprotein
NO: 363 B23, numatrin) SG364 SEQ ID 9235 IL32 Interleukin 32 NO:
364 SG365 SEQ ID 4926 NUMA1 Nuclear protein of the myotic apparatus
1 NO: 365 SG366 SEQ ID 5452 POU2F2 transcription factor with POU
domain, of NO: 366 class 2, 2 SG367 SEQ ID 5452 POU2F2
transcription factor with POU domain, of NO: 367 class 2, 2 SG368
SEQ ID 4968 OGGI 8-oxoguanine-DNA-glycosilase NO: 368 SG369 SEQ ID
1030 CDKN2B Cyclin-dependent kinase inhibitor 2B (p15, NO: 369
inhibits CDK4) SG370 SEQ ID 1029 CDKN2A Cyclin-dependent kinase
inhibitor 2A NO: 370 (melanoma, p16, inhibits CDK4) SG371 SEQ ID
1031 CDKN2C Cyclin-dependent kinase inhibitor 2C (p18, NO: 371
inhibits CDK4) SG372 SEQ ID 1026 CDKN1A Cyclin-dependent kinase
inhibitor 1A (p21, NO: 372 Cip1) SG373 SEQ ID 1027 CDKN1B
Cyclin-dependent kinase inhibitor 1B (p27, NO: 373 Kip1) SG374 SEQ
ID 8851 CDK5R1 Cyclin-dependent kinase 5, regulator NO: 374 subunit
1 (p35) SG375 SEQ ID 10210 TOPORS Of binding to topoisomerase I,
rich inc NO: 375 arginine/serine SG376 SEQ ID 991 P55CDC CDC20
(cell division cycle 20, S. cerevisiae, NO: 376 homologue) SG377
SEQ ID 1028 CDKN1C Cyclin-dependent kinase inhibitor 1C (p57, NO:
377 Kip2) SG378 SEQ ID 7161 TP73 Tumour protein p73 NO: 378 SG379
SEQ ID 5079 PAX5 Paired box gene 5 (specific activating NO: 379
protein of the B lymphocytes line) SG380 SEQ ID 5087 PBX1
Transcription factor of B 1 prelymphocytes NO: 380 leukemia SG381
SEQ ID 5090 PBX3 Transcription factor of B prelymphocytes NO: 381
leukemia B 3 SG382 SEQ ID 5089 ENPP1 Ectonucleotide NO: 382
pyrophosphatase/phosphodiesterase 1 SG383 SEQ ID 5167 PCA1
Ectonucleotide NO: 383 pyrophosphatase/phosphodiesterase 1 SG384
SEQ ID 5111 PCNA Nuclear antigen of proliferating cells NO: 384
SG385 SEQ ID 5159 PDGFRB Platelet-derived growth factor receptor,
beta NO: 385 polypeptide SG386 SEQ ID 5588 PRKCQ kinase C protein,
theta NO: 386 SG387 SEQ ID 5347 PLK1 Plasminogen activator,
urokinase NO: 387 SG388 SEQ ID 5371 PML Promielocytic leukemia NO:
388 SG389 SEQ ID 23532 PRAME Antigen expressed preferentially in
NO: 389 melanoma SG390 SEQ ID 5584 PRKCI protein kinase C, iota NO:
390 SG391 SEQ ID 5728 PTEN Phosphatase and homologue to tensin NO:
391 (mutated in multiple advanced cancers 1) SG392 SEQ ID 5742
PTGS1 prostaglandin-endoperoxide synthase 1 NO: 392 (prostaglandin
G/H synthase and cyclooxigenase) SG393 SEQ ID 5744 PTHLH Hormone
similar to the parathyroidal NO: 393 hormone SG394 SEQ ID 6688 SPI1
Oncogene of integration of provirus of focus NO: 394 forming virus
in the spleen (SFFV) spi1 SG395 SEQ ID 2185 PTK2B Thyrosine kinase
2 beta protein NO: 395 SG396 SEQ ID 5889 RAD51 Homologue to RAD51
(S. cerevisiae) NO: 396 (homologue to RecA of E. coli) SG397 SEQ ID
5896 RAG1 Recombination activator gene 1 NO: 397 SG398 SEQ ID 5914
RARA Retinoic acid receptor, alpha NO: 398 SG399 SEQ ID 3845 KRAS2
Homologue to the viral oncogene of Kirsten NO: 399 2 V-Ki-ras2 rat
sarcoma SG400 SEQ ID 5925 RB1 Retinoblastoma 1 (including
osteosarcoma) NO: 400 SG401 SEQ ID 7422 VEGF Vascular endothelial
growth factor NO: 401 SG402 SEQ ID 7791 ZYX Zyxin NO: 402 SG403 SEQ
ID 940 CD28 Antigen CD28 (Tp44) NO: 403 SG404 SEQ ID 940 CD28
Antigen CD28 (Tp44) NO: 404 SG405 SEQ ID 1656 RBBP4 retinoblastoma
4 binding protein NO: 405 SG406 SEQ ID 1656 DDX6 Polypeptide with
DEAD/H box (Asp-Glu- NO: 406 Ala-Asp/His) 6 (RNA helicase, 54 kD)
SG407 SEQ ID 5928 APEX APEX nuclease (multifunctional DNA repair
NO: 407 enzyme DNA) SG408 SEQ ID 5977 DPF2 D4, family 2 with zinc
fingers and double NO: 408 PHD SG409 SEQ ID 5996 RGS1 G protein
signalling regulator G 1 NO: 409 SG410 SEQ ID 3161 HMMR Motility
receptor mediated by hyaluronane NO: 410 (RHAMM) SG411 SEQ ID 6777
STAT5B signal transducer and transcription activator NO: 411 5B
SG412 SEQ ID 332 BIRC5 Which contains IAP repetitions of NO: 412
baculovirus 5 (survivin) SG413 SEQ ID 6886 TAL1 Acute lymphocytic
leukemia of T NO: 413 lymphocytes 1 SG414 SEQ ID 10482 NXF1 RNA
exportation nuclear factor of RNA 1 NO: 414 SG415 SEQ ID 8115 TCL1A
Leukemia/lymphoma of T 1A lymphocytes NO: 415 SG416 SEQ ID 6955
TRA@ T locus alpha lymphocyte receptor NO: 416 SG417 SEQ ID TCR
beta mRNA of the beta chain of the T NO: 417 lymphocyte receptor
(TCRB) of Homo sapiens SG418 SEQ ID 1791 DNTT Deoxynucleotidyl
transferase, terminal NO: 418 SG419 SEQ ID 7015 TERT Inverse
telomerase transcriptase NO: 419 SG420 SEQ ID 2066 ERBB4 Similar to
the homologue to the viral NO: 420 oncogene of avian erythroblastic
leukemia V-erb-a 4 SG421 SEQ ID 2064 ERBB2 Homologue to the to the
viral oncogene of NO: 421 avian erythroblastic leukemia V-erb-b2 2
(homologue to the oncogene derived from neuro/glioblastoma) SG422
SEQ ID 1956 EGFR Epidermal growth factor receptor NO: 422
(homologue to the viral oncogene of avian erythroblastic leukemia
(v-erb-b)) SG423 SEQ ID 7066 THPO Thrombopoietin (oncogene ligand
of the NO: 423 myeloproliferative leukemia virus, growth factor and
development of megakaryocytes) SG424 SEQ ID 7074 TIAM1 Invasion and
metastasis of lymphoma of T NO: 424 lymphocytes 1 SG425 SEQ ID 7083
TK1 Thymidine kinase 1, soluble NO: 425 SG426 SEQ ID 7132 TNFRSF1A
Tumour necrosing factor receptor NO: 426 superfamily, member 1A
SG427 SEQ ID 7153 TOP2A Topoisomerase (DNA) II alpha (170 kD) NO:
427 SG428 SEQ ID 1052 CEBPD binding protein to CCAAT/enhancer NO:
428 (C/EBP), delta SG428 SEQ ID 9214 FAIM3 Apoptosis inhibitor
molecule mediated by NO: 428 Fas 3 SG429 SEQ ID 5358 PLS3 Plastin 3
(isoform T) NO: 429 SG430 SEQ ID 8717 TRADD associated to TNFRSF1A
via the cell death NO: 430 domain SG431 SEQ ID 8743 TNFSF10 Tumour
necrosing factor superfamily NO: 431 (ligand) member 10 SG432 SEQ
ID 10131 TRAP 1 Thermal shock protein 75 NO: 432 SG433 SEQ ID 7057
THBS1 Thrombospondin 1 NO: 433 SG434 SEQ ID 7341 SUMO1 Homologue to
the supressor of mif two 3 NO: 434 SMT3 1 (yeast) SG435 SEQ ID 7405
UVRAG Gene associated to UV radiation resistance NO: 435 SG436 SEQ
ID 7441 VPREB1 Gene of B 1 prelymphocytes NO: 436 SG437 SEQ ID
51384 WNT16 family of MMTV integration site, Wingless- NO: 437
type, member 16 SG438 SEQ ID 7490 WT1 Wilms tumour 1 NO: 438 SG439
SEQ ID 7517 XRCC3 Of repair of X rays which complement the NO: 439
defective repair in Chinese hamster cells 3 SG440 SEQ ID 896 CCND3
Cyclin D3 NO: 440 SG441 SEQ ID 1017 CDK2 Cyclin-dependent kinase 2
NO: 441 SG442 SEQ ID p14ARF Gene p14ARF from Homo sapiens, NO: 442
promoter region, complete sequence SG443 SEQ ID 3070 HELLS
Helicase, specific for lymphoid cells NO: 443 SG444 SEQ ID 2624
GATA2 GATA 1-binding protein 2 NO: 444 SG445 SEQ ID 2623 GATA1 GATA
1-binding protein (globin transcription NO: 445 factor 1) SG446 SEQ
ID 8028 MLLT10 Myeloid/lymphoid leukemia or of mixed line NO: 446
(homologue to trithorax (Drosophila)); translocated to 10 SG447 SEQ
ID 8301 PICALM Clathrin assembly protein which binds to NO: 447
phosphatidylinositol SG448 SEQ ID 3815 KIT Homologue to the viral
oncogene of Hardy- NO: 448 Zuckerman's feline sarcoma 4 V-kit SG449
SEQ ID 3563 IL3RA Interleukin 3 receptor, alpha (low affinity) NO:
449 SG450 SEQ ID 1050 CEBPA binding protein to CCAAT/enhancer NO:
450 (C/EBP), alpha SG451 SEQ ID 3655 ITGA6 Integrin, alpha 6 NO:
451 SG452 SEQ ID 84955 CML66 Tumour antigen of chronic myelogenous
NO: 452 leukemia 66 SG453 SEQ ID 7187 TRAF3 Factor associated to
the TNF receptor 3 NO: 453 SG454 SEQ ID 1612 DAPK1 Kinase protein
associated to cell death 1 NO: 454 SG455 SEQ ID 8788 MAP3K12
Homologue similar to Delta (Drosophila) NO: 455 SG456 SEQ ID 5591
PRKDC Kinase protein, activated by DNA, catalytic NO: 456
polypeptide SG457 SEQ ID 1789 DNMT3B
(cytosine-5-)-methyltransferase 3 beta of NO: 457 DNA SG458 SEQ ID
2950 GSTP1 Glutathion S-transferase pi NO: 458 SG459 SEQ ID 3122
HLA-DRA Complex greater than histocompatibility, NO: 459 class II,
DR alpha SG460 SEQ ID 3206 HOXA10 Homeotic box A10 NO: 460 SG461
SEQ ID 3394 IRF8 Binding protein to the agreed sequence of NO: 461
interferon 1 SG462 SEQ ID 3398 ID2 DNA binding inhibitor 2,
negative dominant NO: 462 helix-loops-helix protein SG463 SEQ ID 60
ACTB Actin, beta NO: 463 SG464 SEQ ID 60 ACTB Actin, beta NO: 464
SG465 SEQ ID 2868 GRK4 Kinase of receptor coupled to a protein G 4
NO: 465 SG466 SEQ ID 2597 GAPD Glyceraldehyde-3-phosphate NO: 466
dehydrogenase SG467 SEQ ID 2597 GAPD Glyceraldehyde-3-phosphate NO:
467 dehydrogenase SG468 SEQ ID 6772 STAT1 Signal transducer and
transcription activator NO: 468 1, 91 kDa SG469 SEQ ID 18S rRNA
Human rRNA gene 18S
NO: 469 SG470 SEQ ID 7037 TFRC Transferrin receptor (p90, CD71) NO:
470 SG471 SEQ ID 28S rRNA Human ribosomal RNA gene 28S NO: 471
SG472 SEQ ID 6168 RPL37A Ribosomal protein L37a NO: 472 SG473 SEQ
ID 6171 RPL41 Ribosomal protein L41 NO: 473 SG474 SEQ ID 3191 HNRPL
Heterogeneous nucler ribonucleoprotein L NO: 474 SG475 SEQ ID 3608
ILF2 Binding factor to the interleukin-2 enhancer, NO: 475 45 kD
SG476 SEQ ID 8407 TAGLN2 Transgelin 2 NO: 476 SG477 SEQ ID 824
CAPN2 Calpain 2, (m/II) major subunit NO: 477 SG478 SEQ ID 5686
PSMA5 Subunit of proteasome (prosome, NO: 478 macropain), type
alpha, 5 SG479 SEQ ID 27254 PMM1 Phosphomannomutase 1 NO: 479 SG480
SEQ ID 8079 MLF2 Myeloid leukemia factor 2 NO: 480 SG481 SEQ ID
5501 PPP1CC Phosphatase protein 1, catalytic subunit, NO: 481 gamma
isoform SG482 SEQ ID 22794 CASC3 Candidate for susceptibility to
cancer 3 NO: 482 SG483 SEQ ID 23164 KIAA0864 Protein KIAA0864 NO:
483 SG484 SEQ ID 7296 TXNRD1 Thioredoxine reductase 1 NO: 484 SG485
SEQ ID 5713 PSMD7 Subunit of proteasome (prosome, NO: 485
macropain) 26S, no-ATPase, 7 (homologue to Mov34) SG486 SEQ ID 8892
EIF2B2 initiation factor of eukaryotic translation 2B, NO: 486
subunit 2 (beta, 39 kD) SG487 SEQ ID 3105 HLA-A Complex greater
than histocompatibility, NO: 487 class I, A SG488 SEQ ID 4176 MCM7
Minichromosome maintenance deficient (S. cerevisiae) 7 NO: 488
SG489 SEQ ID 8718 TNFRSF25 Tumour necrosing factor receptor NO: 489
superfamily, member 25 SG490 SEQ ID 3958 LGALS3 Lectin, which binds
to galactosides, soluble, NO: 490 3 (galectin 3) SG491 SEQ ID 311
HLA-DPA1 Complex greater than histocompatibility, NO: 491 class II,
DP alpha 1 SG492 SEQ ID 5328 PLAU Plasminogen activator, urokinase
NO: 492 SG493 SEQ ID 1281 COL3A1 Collagen, type III, alpha 1
(Ehlers-Danlos NO: 493 type IV syndrome, dominant autosomal) SG494
SEQ ID 287 ANK2 Ankyrin 2, neuronal NO: 494 SG495 SEQ ID 327657
SERPINA9 serine (or cysteine) proteinase inhibitor, NO: 495 clade A
(alpha-1 antiproteinase, antitrypsin), member 9 SG496 SEQ ID 10360
NPM3 Nucleophosmin/nucleoplasmin 3 NO: 496 SG497 SEQ ID 1235 CCR6
Receptor 6 of chemokenes (motive C-C) NO: 497 SG498 SEQ ID 3055 HCK
Hematopoietic cell kinase NO: 498 SG499 SEQ ID 26354 GNL3 similar
to guanine 3 nucleotide binding NO: 499 protein (nucleolar) SG500
SEQ ID 2885 GRB2 Protein bound to growth factor receptor 2 NO: 500
SG501 SEQ ID 597 BCL2A1 protein related to BCL2 A1 NO: 501 SG502
SEQ ID 1997 ELF1 Factor similar to E74 1 (transcription factor NO:
502 with ets domain) SG503 SEQ ID 1508 CTSB Catepsin B NO: 503
SG504 SEQ ID 257144 GCET2 transcript expressed in the budding
centre 2 NO: 504 SG505 SEQ ID 2335 FN1 Fibronectin 1 NO: 505 SG506
SEQ ID 5133 PDCD1 Programme cell death 1 NO: 506 SG507 SEQ ID 3125
HLA-DRB3 Complex greater than histocompatibility, NO: 507 class II,
DR beta 3 SG508 SEQ ID 3117 HLA-DQA1 Complex greater than
histocompatibility, NO: 508 class II, DQ alpha 1 SG509 SEQ ID
257144 GCET2 transcript expressed in the budding centre NO: 509
germinal 2 SG510 SEQ ID 327657 SERPINA9 serine (or cysteine)
proteinase inhibitor, NO: 510 clade A (alpha-1 antiproteinase,
antitrypsin), member 9 SG511 SEQ ID 1033 CDKN3 Cyclin dependent
kinases 3 (phosphatase NO: 511 of dual specificity associated CDK2)
SG512 SEQ ID 1997 ELF1 Factor similar to E74 1 (transcription
factor NO: 512 with ets domain) SG513 SEQ ID 1509 CATSD Catepsin D
(liposomal aspartylprotease) NO: 513 SG514 SEQ ID 3315 HSPB1
Thermal shock protein of 27 kD 1 NO: 514 SG515 SEQ ID 87 ACTN1
Actinin, alpha 1 NO: 515 SG516 SEQ ID 654 BMP6 Morphogenetic bone
protein 6 NO: 516 SG517 SEQ ID 9780 FAM38A family with similarity
of sequence 38, member A NO: 517 SG518 SEQ ID 962 CD48 Antigen CD48
(membrane protein of B NO: 518 lymphocytes) SG519 SEQ ID 3566 IL4R
Interleukin 4 receptor NO: 519 SG520 SEQ ID 1821 DRP2 Dystrophin
related protein 2 NO: 520 SG521 SEQ ID 3726 JUNB Jun B
Proto-oncogene NO: 521 SG522 SEQ ID 6279 S100A8 Calcium-binding
protein S100 A8 NO: 522 (calgranuline A) SG523 SEQ ID 10320 ZNFN1A1
Protein with zinc fingers, subfamily 1A, 1 NO: 523 (lkaros) SG524
SEQ ID 10461 MERTK Thyrosine kinase of the C-mer proto- NO: 524
oncogene SG525 SEQ ID 51621 KLF13 Factor similar to that of Kruppel
13 NO: 525 SG526 SEQ ID 865 CBFB Nucleus-binding factor, beta
subunit NO: 526 SG527 SEQ ID 1051 CEBPB binding protein to
CCAAT/enhancer NO: 527 (C/EBP), beta SG529 SEQ ID 7024 TFCP2
Transcription factor CP2 NO: 529 SG530 SEQ ID 1385 CREB1 CAMP
response element binding protein NO: 530 SG531 SEQ ID 4782 NFIC I/C
nuclear factor (CCAAT binding factor NO: 531 transcription factor)
SG532 SEQ ID 2553 GABPB2 Transcription factor of the protein which
NO: 532 binds to GA, beta 2 subunit (47 kD) SG533 SEQ ID 1958 EGR1
Early growth response 1 NO: 533 SG534 SEQ ID 10661 KLF1 Factor
similar to that of Kruppel 1 NO: 534 (erythroid) SG535 SEQ ID 1997
ELF1 Factor similar to E74 1 (transcription factor NO: 535 with ets
domain) SG536 SEQ ID 2113 ETS1 homologue to the E26 oncogene of NO:
536 erythroblastosis virus v-ets 1 (avian) SG537 SEQ ID 2114 ETS2
homologue to the E26 oncogene of NO: 537 erythroblastosis virus
v-ets 2 (avian) SG538 SEQ ID 2313 FLI1 Integration of Friend 1
leukemia virus NO: 538 SG539 SEQ ID 2625 GATA3 GATA 3 binding
protein NO: 539 SG540 SEQ ID 862 CBFA2T1 Nucleus binding factor,
runt domain, alpha NO: 540 2 subunit; translocated to 1; related to
cyclin D SG541 SEQ ID 3091 HIF1A Factor inducible by hypoxia 1,
alpha subunit NO: 541 (basic transcription factor of helix-loops-
helix) SG542 SEQ ID 6927 TCF1 Transcription factor 1, hepatic;
LF-B1, NO: 542 hepatic nuclear factor (HNF1), proximal factor of
albumin SG543 SEQ ID 3234 HOXD8 Homeotic box D8 NO: 543 SG544 SEQ
ID 3235 HOXD9 Homeotic box D9 NO: 544 SG545 SEQ ID 9935 MAFB Family
of the oncogene of NO: 545 musculoaponeurotic fibrosarcoma (avian)
V-maf SG546 SEQ ID 7975 MAFK Family of the oncogene of NO: 546
musculoaponeurotic fibrosarcoma (avian) V-maf, protein K SG547 SEQ
ID 8721 EDF1 factor related to edothelialdifferentiation 1 NO: 547
SG548 SEQ ID 2000 ELF4 Factor similar to E74 4 (transcription
factor NO: 548 with ets domain) SG549 SEQ ID 7593 ZNF42 Protein
with zinc fingers 142 (clone pHZ-49) NO: 549 SG550 SEQ ID 4763 NF1
neurofibromin 1 NO: 550 SG551 SEQ ID 4772 NFATC1 Nuclear factor of
activated T-lymphocytes, NO: 551 cytoplasmic, calcineurin
1-dependent SG552 SEQ ID 5080 PAX6 Paired box gene 6 (aniridia,
keratitis) NO: 552 SG553 SEQ ID 7849 PAX8 Paired box gene 8 NO: 553
SG554 SEQ ID 57026 PLP Pyridoxal (pyridoxine, vitamin B6) NO: 554
phosphatase SG555 SEQ ID 2274 PLZF With four LIM domains and
average 2 NO: 555 SG556 SEQ ID 5950 RBP4 Retinol 4-binding protein,
plasma NO: 556 SG557 SEQ ID 6095 RORA Orphan receptor related to
RAR A NO: 557 SG558 SEQ ID 6667 SP1 Transcription factor Sp1 NO:
558 SG559 SEQ ID 6772 STAT1 Signal transducer and transcription
activator NO: 559 1, 91 kDa SG560 SEQ ID 6908 TBP TATA box-binding
protein NO: 560 SG561 SEQ ID 6932 TCF7 Transcription factor 7 (T
lymphocyte NO: 561 specific, box HMG) SG562 SEQ ID 51513 ETV7 Gene
variant of ets 7 (oncogene TEL2) NO: 562 SG563 SEQ ID 7535 ZAP70
Zeta chain associated kinase protein (TCR) NO: 563 (70 kD)
[0145] From among these genes, four of them (ACTB, GAPD, 18S rRNA
and 28S rRNA), do not have a special relation with neoplasias and
were initially included in the microarray because, for a long time,
it was believed that their expression remained constant and they
were used when normalizing the microarray data: they are the type
of genes alluded to when we speak of "constitutive" genes at other
points in the specification. At present, it is not thought that
there is a gene whose expression remains constant in any
circumstance, for which reason, in the present study, the genes
ACTB, GAPD, 18S rRNA and 28S rRNA have received the same treatment
as the other genes of the microarray, except for the fact that the
first two of them have been used as integrity controls, as
described further on.
[0146] In Table 1 it can be observed that there are genes which are
represented by more than one oligonucleotide. This is the case
because the existence of two or more probes per gene can be used to
measure the integrity of the synthesized cRNA. The genes for which
more than one oligonucleotide have been designed to act as probe,
each one of which hybridizes with a different sequence, are
indicated below in Table 2.
TABLE-US-00002 TABLE 2 Genes represented by more than one
oligonucleotide as probe Usual abbreviation of the gene Probe1
Probe2 Probe3 ABL1 SG10 SG180 BCR SG169 SG170 CBFB SG189 SG526 CD28
SG403 SG404 EIF4E SG293 SG305 ELF1 SG512 SG535 SG502 ETS2 SG95
SG537 GCET2 SG504 SG509 MAFB SG258 SG545 MTCP1 SG358 SG359 POU2F2
SG366 SG367 RGS1 SG56 SG409 S100A2 SG35 SG71 SNRPB SG142 SG143
STAT1 SG77 SG559 SG468 TIA-2 SG7 SG73 TAGLN2 SG24 SG476 TCF3 SG277
SG279 XRCC5 SG32 SG330 ZYX SG97 SG402 CD44 SG228 SG229 ACTB SG463
SG464 GAPD SG464 SG467
Establishment of Control Probes
[0147] To decrease the variability, a large number of controls were
included in each microarray. These controls suppose an objective
measurement on the process quality, and therefore, of the quality
of the data obtained. They are of several types and origins:
[0148] a) Probes Used as Integrity Controls
[0149] These probes were 2 pairs of oligonucleotides complementary
to ends 5' and 3' of the .beta.-actin genes (probes code SG463 and
SG464) and glyceraldehyde-3-phosphate dehydrogenase (probes code
SG466 and SG467). The ratio between the intensities of the probe
located at end 3' and 5' makes it possible to check the quality of
the starting RNA and the functioning of the labelling reaction. The
details on these oligonucleotides appear in Table 3.
TABLE-US-00003 TABLE 3 Oligonucleotides used as integrity controls
Oligo- Gene GenID nucleotide SEQ ID NO: Source gene Abbreviation
No. SG463 SEQ ID .beta.-actin ACTB 60 NO: 463 SG464 SEQ ID
.beta.-actin ACTB 60 NO: 464 SG466 SEQ ID Glyceraldehyde-3- GAPD
2597 phosphate NO: 466 dehydrogenase SG467 SEQ ID Glyceraldehyde-3-
GAPD 2597 phosphate NO: 467 dehydrogenase
b) Probes Used as Negative Controls
[0150] These probes are largely formed by a group of
oligonucleotides of 50 nucleotides (50-mer) which are not
complementary to any known human sequence. For them, the BLAST tool
was applied to these probes and it was observed that they did not
hybridize with any human sequence. They are identified with codes
SC1 (SEQ ID NO:564), SC2 (SEQ ID NO:565), SC3 (SEQ ID NO:566), SC4
(SEQ ID NO:567), SC5 (SEQ ID NO:568), SC6 (SEQ ID NO:569) and SC7
(SEQ ID NO:570) and oligonucleotides SCN1 (SEQ ID NO:571), SCN5
(SEQ ID NO:575), SCN7 (SEQ ID NO:577) and SCN10 (SEQ ID NO:580) are
also used as negative controls. They are used to determine the
optimum conditions of hybridization, washing and developing of the
chips or microarrays. The appearance of a signal associated to them
indicates the existence of non-specific hybridization.
[0151] c) Exogenous Probes Used as Internal Positive Controls:
"Spiked Controls"
[0152] "Spiked controls" are synthetic oligonucleotides whose
sequence coincides with a fragment of a transcript of a non-human
gene or of any other sequence of nucleotides of low homology with
transcripts of human genes which is polyadenylated at 3', which is
used as positive control, in the determination of the process
quality, in the normalization of data and for the establishment of
the linear range of the process (Benes V et al., 2003). To do this,
the transcripts or corresponding polyadenylated sequences are added
to the total starting RNA before starting the labelling process,
and therefore, they suffer the same reactions (labelling,
hybridization and developing) as the total
[0153] RNA of the samples.
[0154] 7 "Spiked controls" are used. To ensure low homology with
human genes 5 transcripts of Bacillus subtilis genes (dap, thr,
trp, phe and lys) and 2 transcripts of genes of the Sharkav virus
are used, frequently referred to as "Plum poxvirus" (Sppv), which
is a plant virus. The details on these oligonucleotides are shown
below in Table 4. The ATCC (American Type Culture Collection)
numbers which appear after the name of the source genes refer to
the identification number in the ATCC of E. coli strains containing
recombinant plasmids which contain the sequence of the genes from
which the transcripts added to the RNA are obtained and which were
also used for the design of the sequences of the corresponding
oligonucleotides bound to the microarray.
TABLE-US-00004 TABLE 4 Oligonucleotides used as "Spiked Controls"
Concentration Transcript (pM) in the Oligo- Gene Bank size "spiked
controls" nucleotides SEQ ID NO: Source gene code (nt) solution
SSPC1 SEQ ID Dap L38424 1820 2000 NO: 584 (ATCC no. 87486) SSPC2
SEQ ID Lys X17013 1000 1250 NO: 585 (ATCC no. 87482) SSPC3 SEQ ID
Thr X04603 1980 5 NO: 586 (ATCC no. 87484) SSPC4 SEQ ID Plum pox
virus, AF401296 100 NO: 587 isolated PENN2 (Sppv1) SSPC5 SEQ ID
Plum pox potyvirus, X57975 750 NO: 588 mRNA coated protein (Sppv2)
SSPC6 SEQ ID Phe M24537 1320 1000 NO: 589 (ATCC no. 87483) SSPC7
SEQ ID Trp K01391 2500 500 NO: 590 (ATCC no. 87485)
[0155] c. 1.: Preparation of the 5 "Spiked controls" of Bacillus
subtilis
[0156] The E. coli bacteria with the recombinant plasmids were
acquired from ATCC (Rockville, Md. USA) The plasmids (pBluescript
II-KS) contained the cloned cDNA of a Bacillus subtilis gene, with
cut-off sites for the NotI enzymes at end 5' and BamHI at end 3'
and a poly extension (dA) prior to the cut-off site for BamHI.
[0157] After reconstituting and allowing the cells to grow during
the night at 37.degree. C. in LB+Ampicillin medium, the plasmid was
obtained with the Midipreps kit (Jetstar) following the
manufacturer's recommendations. 10 .mu.g of each one of the
plasmids was linearized by digestion with 30 U of NotI restriction
enzyme, in the presence of 1XNE3 and 1XBSA buffer during 3 hours at
37.degree. C. The linearized plasmids were subjected to extraction
with phenol:chloroform:isoamilic alcohol (Ambion), precipitation
with 0.1 vol of 3M sodium acetate (Sigma) and 2.5 vol of 100%
Ethanol and elimination of salts with 80% Ethanol, following the
aforementioned protocol. The DNA obtained was resuspended in 10
.mu.l of RNase-free water.
[0158] Next, the transcripts with sense were synthesized with an in
vitro transcription reaction (I.V.T) from 1 .mu.g of plasmid
linearized using the MegaScript T3 kit (Ambion) and following the
manufacturer's recommendations. The plasmids obtained were purified
with the RNeasy Total RNA Isolation Kit (QIAGEN), following the
manufacturer's recommendations.
[0159] The quantification, determination of the purity, quality and
size of the transcripts obtained were performed following the same
methods which are described below for the total RNA.
[0160] c.2. Preparation of the 2 "Spiked Controls" which Represent
SPPV Genes
[0161] The recombinant plasmids (Progenika Biopharma) contained the
cloned
[0162] cDNA of the two sppvl and sspv2 genes inserted between two
PvuII and PstI restriction sites. End 3' of each insert contains a
polyadenylation extension.
[0163] JM109 cells were transformed with the plasmids which
contained the transcripts. The cells were left to grow in plates
with LB+Ampicillin medium at 37.degree. C., the colonies with the
transferred cells were selected and they were grown in LB+AMP
liquid medium.
[0164] The recovery of the plasmids was performed with the
Midipreps Plasmid Purification kit (Qiagen), following the
manufacturer's recommendations. 10 .mu.g of each plasmid was
linearized with 30 U of the PvuII restriction enzyme. The insert
was extracted with phenol:chloroform:isoamilic alcohol (Ambion),
precipitation with 0.1 volumes of 7.5 M sodium acetate and 2.5
volumes of 100% ethanol. The salts were eliminated by two washings
with 80% ethanol. The DNA obtained was resuspended in 10 .mu.l of
Rnase-free water.
[0165] Next, the transcripts with sense were synthesized with 1
.mu.g of plasmid linearized using the T7 MegaScript kit (Ambion)
and following the manufacturer's recommendations. The product of
the reaction was cleaned with the RNeasy Total RNA Isolation Kit
(Qiagen).
[0166] The quantification, measuring of the purity of the
transcripts obtained and verification of their size were then
performed
[0167] A solution of "Spiked controls" was prepared from the
transcripts obtained with different concentrations of each one of
those "spiked" (see Table 3), so that they covered the whole range
of intensities of the "scanner" reader system (values of intensity
which go from 0 to 65,535 in arbitrary units). This solution was
added in the same quantity to 5.quadrature. .mu.g of total starting
RNA from each sample before starting the process.
[0168] c.3. Design of Probes Representative of Each One of the
Transcripts:
[0169] So that the behaviour of the probes was as similar as
possible to the probes designed for the genes to be studied, with
the Oligo 6.0 programme (M.B.I), those sequences were selected for
each "Spiked control" which complied with the same requirements
established for the probes of the genes represented (length, GC
content, "sense" strand and distance to end 3') and which did not
form stable loops (energy less than -7 Kcal/mol). The BLAST tool
was applied to the sequences which complied with those requirements
and that with less homology with human sequences was chosen.
[0170] After depositing and immobilizing the probes corresponding
to the "Spiked controls" on the glass, it was verified: a) that the
probes did not hybridrize in non-specific manner with the samples
to analyse, b) that all the probes had similar hybridization
characteristics, and c) that the signal of intensity obtained from
each one of them can be related to the quantity of transcript added
to the RNA.
[0171] d) Hybridization Controls
[0172] Snthetic oligonucleotides of DNA with 70 nucleotides
(70-mer) were used As hybridization controls, modified at one end
with a biotin molecule. These molecules are added in the same
quantity to the sample just before hybridization, so that their
value only depends on the processes of hybridization, developing
and capture of images of the microarray. For each one of these
70-mer oligonucleotides, on the microarray there are several copies
of an oligonucleotide with 50 nucleotides in length (50-mer),
complementary to the corresponding 70-mer oligonucleotide with
which it must hybridize. The 50-mer oligonucleotides which form
part of the microarray and which are complementary to 70-mer
oligonucleotides which are added to the cRNA before hybridizing are
of codes SCN2, SCN3, SCN6, SCN8, SCN11, SCN12 and
[0173] SCN13. To ensure low homology with human sequences, the
sequences of these oligonucleotides were obtained from sequences of
Arabidopsis thaliana and Tripanosoma brucei. Their characteristics
appear in Table 5
TABLE-US-00005 TABLE 5 Oligonucleotides used in the microarray as
positive hybridization controls 50-mer oligonucleotide
Complementary present in GenBank 70-mer the microarray SEQ ID NO:
Source gene code oligonucleotide SCN2 SEQ ID NO: 572 Alpha-1.4-
AY026941 C2 fucosyltransferase (FT4-M) from Arabidopsis thaliana
SCN3 SEQ ID NO: 573 mRNA of the AJ239128 C3 thioredoxine of
Tripanosoma brucei SCN6 SEQ ID NO: 576 mRNA from a supposed
AY051079 C6 expression protein of the RBP (complete CDS) from
Arabidopsis thaliana SCN8 SEQ ID NO: 578 mRNA from a supposed
AY045879 C8 transfer protein of lipids (At1g48750) (complete CDS)
from Arabidopsis thaliana SCN11 SEQ ID NO: 581 mRNA from a supposed
AY045879 C11 transfer protein of lipids (At1g48750) (complete CDS)
from Arabidopsis thaliana SCN12 SEQ ID NO: 582 mRNA from a supposed
AY045879 C12 transfer protein of lipids (At1g48750) (complete CDS)
from Arabidopsis thaliana SCN13 SEQ ID NO: 583 mRNA of the papain-
AF191028 C13 type cysteine endopeptidase XCP2 (complete CDS) from
Arabidopsis thaliana
[0174] For the design of the 50-mer oligonucleotides it was
verified, in a manner similar to that previously described for the
"Spiked controls", that the oligonucleotides to be used did not
hybridize in non-specific form with the samples to be analysed,
that all the probes had similar hybridization characteristics and
that the signal of intensity obtained from each one of them could
be related to the quantity of the corresponding 70-mer
oligonucleotide added to the cRNA. This made it possible to take as
valid the oligonucleotides indicated in Table 5. The SCN4 (SEQ ID
NO:574) and SCN9 (SEQ ID NO:579) oligonucleotides, designed in
principle to act as hybridization controls, were seen to produce
specific hybridization when human cRNA hybridized, for which reason
they also appear in the microarray, as if they were probes which
represent a human gene, but they are not taken into account as
positive hybridization controls. For their part, oligonucleotides
SCN1 (SEQ ID NO:571), SCN5 (SEQ ID NO:575), SCN7 (SEQ ID NO:577)
and SCN10 (SEQ ID NO:580), which did not hybridize either in
non-specific form with the samples, are also present in the
microarray as negative hybridization controls, as no
oligonucleotide complementary thereto were added to the cRNA.
[0175] For its part, the hybridization controls solution, which
contained the 70-mer oligonucleotides complementary to the 50-mer
oligonucleotides present in the microarray as positive
hybridization controls, was prepared from the corresponding
biotinylated 70-mer sequences using a different concentration for
each one of them, as shown in Table 6:
TABLE-US-00006 TABLE 6 Composition of the positive hybridization
controls solution 70-mer Oligonucleotide Complementary
Concentration (pM) added to the 50-mer in the hybridization cRNA
SEQ ID NO: oligonucleotide control solution C2 SEQ ID NO: 591 SCN2
750 C3 SEQ ID NO: 592 SCN3 250 C6 SEQ ID NO: 593 SCN6 1500 C8 SEQ
ID NO: 594 SCN8 1250 C11 SEQ ID NO: 595 SCN11 2000 C12 SEQ ID NO.
596 SCN12 4500 C13 SEQ ID NO: 597 SCN13 2500
Blanks
[0176] Dimethyl sulfoxide (DMSO) without any probe was used, as
this is the solvent wherein the oligonucleotides are found at the
time of being deposited on the surface of the microarray.
Description of the Microarray Device
[0177] Twelve replicas of each probe were deposited in different
localizations on the surface of a solid support (glass in similar
form to a microscope slide) using Microgrid II Spoter
(Biorobotics). The 12 replicas of each probe were distributed on
the support at random: 6 in the upper area and 6 in the lower area.
Aminosylanized glass (Corning) was used as solid support. The
moisture and the temperature were controlled throughout the
printing process.
[0178] The covalent binding of the probes to the solid supports was
carried out by cross-linking by ultraviolet radiation using the
"Stratalinker" apparatus (Stratagene).
[0179] The quality control of the production process of the
microarrays was the following: a) In each production run a
microarray was stained with ethydium bromide which made it possible
to analyze the size and form of the points printed. b) Another
array of each run was hybridized with an already hybridized cRNA,
analysing the hybridization signal, the background noise and the
reproducibility of the replicas.
[0180] The characteristics of the array are shown below in Table
7:
TABLE-US-00007 TABLE 7 Characteristics of the microarray Number of
genes represented 538 Length of the oligonucleotides 25-55 mer
Strand analysed Sense Number of oligonucleotides per gene 1 (except
21 genes which are represented by 2 or 3 different
oligonucleotides) Number of replicas of each oligonucleotide 12
Blank DMSO Integrity controls 4 Spiked controls (internal positive
controls) 7 Positive hybridization controls 9 Negative controls 11
Total number of points 8192 (32 areas .times. 16 .times. 16) Size
of the microarray 25 .times. 75 mm Area spotted 16.38 .times. 17.82
mm Distance between points x- y- axis 360 .mu.m
Treatment of the Samples
Cell Cultures
[0181] Cultures of Jurkat cells (cell line from Leukemia T) and
U937 (cell line from promonocytic leukemia) were centrifuged for 10
minutes at 1200 rpm and, after decanting the supernatant, the
precipitate was resuspended in RNAlater (Ambion Inc) and it was
stored at -80.degree. C. at the time of extraction of the RNA. The
RNA was extracted with TRIzol (Gibco-BRL Carlbad, Calif., USA)
following the manufacturer's recommendations.
Blood Samples
[0182] The blood samples were directly collected in PAXgene Blood
RNA Tubes-PreAnalytix (Qiagen) tubes. 2.5 ml of blood were
extracted in each tube and two tubes per individual. The tubes were
inverted several times to allow the blood to mix with the
stabilizing liquid which the tube contains, and they were stored at
-20.degree. C. until the night before RNA extraction.
Extraction of the Total RNA
[0183] The tubes with the sample were incubated at ambient
temperature during the night previous to the RNA extraction. The
PAXgene Blood RNA kit (Qiagen) was used for the extraction
following the manufacturer's recommendations, including the
intermediate step of treatment with DNase (RNase-Free DNase Set,
Quiagen) in column. The RNA of each extraction tube was eluted in
80 .mu.l of BR5 buffer. The RNA of the two tubes which correspond
to each patient was gathered in a single tube.
Purification of the Total RNA
[0184] To ensure that the RNA obtained is free from free from
contaminants that can interfere in later labelling reactions, it
was purified in the following way: 16 .mu.l (0.1 vol) of 7.5 M
sodium acetate (Sigma) and 400 .mu.l (2.5 vol) of 100% ethanol were
added to 160 .mu.l of total RNA solution. The solution was mixed in
a "vortex" stirrer and it was incubated for 1 hour at -20.degree.
C. After 20 minutes of centrifugation at 12,000.times.g at
4.degree. C., the precipitate was washed twice with 500 .mu.l of
80% ethanol and it was resuspended in 35 .mu.l of Rnase-free water.
The RNAs obtained were stored at -80.degree. C. until their later
use.
Quantification of the Total RNA
[0185] The quantification of the total RNA was carried out by the
measurement of the absorbance at 260 nm in a spectrophotometer (DU
65, Beckman Coulter). 2 .mu.l of the total RNA solution were
diluted in 98 .mu.l of 1 mM Tris-HCl pH 7.5 and the concentration
was estimated (.mu.g/ml) taking into account that 1 Unit of Optical
Density at 260 nm corresponds to a RNA concentration of 44
.mu.g/ml.
Determination of the Purity and Quality of the RNA
[0186] The degree of purity was established from the absorbance
ratio A260/A280 (nucleic acid/proteins), considering that the RNA
is suitable, of "good quality", when the A260/A280 ratio is between
1.9 and 2.1.
[0187] The quality of the total RNA was determined by viewing the
RNA after electrophoresis. 500 ng of total RNA were subjected to
electrophoresis in 1% agarose gel (FMC) in TAE 1.times. buffer with
BrEt (0.5 mg/ml), under a potential differenceof 100V for 25
minutes in AC electrophoresis cuvettes (BioRad). As marker of
molecular weights, phage .phi.29 digested with the BamH I
restriction enzyme was used. The gels were viewed in a Gel Doc
(BioRad) ultraviolet light transiluminator.
Sample Labelling
[0188] The choice of the strand with sense as probe limited the
labelling strategy at those approximations which yield an antisense
labelled product (complementary to the probe immobilized on the
solid support).
cRNA Labelling
[0189] This type of labelling was performed during the course of an
amplification process which consists of the use for the synthesis
of single-strand cDNA, of an oligo(dT) primer which contains a
promoter for the polymerase RNA enzyme of the T7 phage, an enzyme
which will be used in the sample amplifications step.
[0190] a.--cDNA synthesis: step wherein DNA (cDNA) complementary to
the starting mRNA was synthesized. 5 .mu.g of total RNA was
incubated with 2 .mu.l of the "Spiked controls" solution and 100
pmol of T7-(dT)24 (Genset Corp) primer in final volume of 12 .mu.l
during 10 minutes at 70.degree. C. in a thermoblock, the mixture
was cooled on ice and 4 .mu.l of 5.times. First Strand Buffer
(Gibco BRL Life Technologies), 0.1M 2 .mu.l DTT (Gibco BRL Life
Technologies), 1 .mu.l dNTP mix 10 mM (Gibco BRL Life Technologies)
and 1 .mu.l of SuperScript II RNase H RT (200 OR/.mu.l) (Gibco BRL
Life Technologies) were added. After 1 hour of incubation in a bath
equipped with a thermostat (Selecta) at 42.degree. C., the reaction
was cooled on ice.
[0191] b.--Double chain DNA synthesis (dsDNA): a double chain of
DNA was synthesized from the cDNA synthesized in the previous step.
To 20 .mu.l of previous reaction were added 91 .mu.l of Rnase-free
water, 30 .mu.l of "Second Strand Reaction buffer" (Gibco BRL Life
Technologies), 3 .mu.l 10 mM dNTPs (Gibco BRL Life Technologies),
10 U E. coli DNA Ligase (Gibco BRL Life Technologies), 40 O E. coli
DNA polymerase I (Gibco BRL Life Technologies), 2 U E. coli RNase H
(Gibco BRL Life Technologies) in a final volume of 150 .mu.l. The
reaction was incubated in a thermoblock at 16.degree. C. for 2
hours. Next, 10 U of T4 DNA Polymerase (Gibco BRL Life
Technologies) were added and the mixture was incubated at
16.degree. C. for 5 minutes. To stop the reaction, 10 .mu.l of 0.5
M EDTA were added.
[0192] c.--Purification of the dsDNA: To eliminate possible remains
of reaction products which may interfere in later labelling
reactions, the DNA obtained through phenol/chloroform extraction
and later precipitation was purified. To 162 .mu.l of previous
reaction 162 .mu.l of phenol: chloroform: isoamilic alcohol
solution (25:24:1) (Ambion) were added. It was centrifuged for 2
min at 12,000.times.g in a centrifuge at ambient temperature, the
upper aqueous phase was collected. To this upper phase 0.5 volumes
of 7.5M ammonium acetate (Sigma Chemical) and 2.5 volumes of 100%
ethanol cooled to -20.degree. C.) were added. After stirring with
"vortex" to mix well the components and centrifugation for 20
minutes at 12000.times.g at ambient temperature, the supernatant
was eliminated and the precipitate was washed twice with 80%
ethanol. The DNA obtained was resuspended in 10 .mu.l of RNase-free
water and it was concentrated in a "Speed-Vac" concentrator to a
volume of 2 .mu.l. This DNase was stored at -20.degree. C. until
its later use.
[0193] d.--Synthesis and labelling of the cRNA: This reaction was
carried out in a volume of 20 .mu.l and using the T7 Megascript kit
(Ambion), following the manufacturer's instructions and
incorporating nucleotides modified with biotin, Bio-11-CTP and
Bio-11 UTP (Perkin Elmer) in non-modified nucleotide/modified
nucleotide ratio of 1:3. The reaction was incubated during 5 h and
15 minutes in a bath with thermostat (Selecta) at 37.degree. C.,
stirring the reaction every 45 minutes. After this incubation, 1
.mu.l of DNase was added and it was incubated for 30 min at
37.degree. C.
[0194] e.--Purification of the biotinylated cRNA: The biotinylated
cRNA was purified with the RNeasy Total RNA Isolation Kit (Qiagen)
following the manufacturer's instructions. The biotinylated cRNAs
obtained were eluted in a volume of 80 .mu.l and they were stored
at -80.degree. C. until its later use.
[0195] The quantity, purity and quality of the cRNA obtained were
determined following the same methods described for the total
RNA.
[0196] The cRNA was stored at -80.degree. C. until its later
use.
Fragmentation of the Biotinylated cRNA
[0197] 10 .mu.g of biotinylated cRNA were fragmented in the
presence of 5.times. (200 mM Tris-acetate, pH 8.1, 500 mM HOAC, 150
mM MgOAc) fragmentation buffer during 35 minutes at 94.degree. C.
in a thermoblock. It was verified that the fragmentation reaction
had been carried out by viewing 1 .mu.l of fragmentation solution
in electrophoresis on 1% agarose gel.
Hybridization of the cRNA Labelled with the Probes of the
Microarray
[0198] In this step the labelled genetic material were placed in
contact with the probes immobilized on the solid support.
[0199] 10 .mu.l of the hybridization control solution were added to
the biotinylated and fragmented cRNA solution and the mixture was
incubated for 3 min at 95.degree. C. to denature the possible
secondary structures. After incubation, the mixture was immediately
taken to ice to prevent the possible renaturing of the sample.
[0200] The hybridization was carried out for 6 hours at 42.degree.
C. in the Ventana Discovery automatic hybridization station
(Ventana Medical Systems). The hybridization and washing buffers
were supplied by Ventana Medical System. The microarrays were
automatically stained in the hybridization station with
streptavidin conjugated with Cy3 (Amersham Biosciences) using the
manufacturer's recommendations.
Capture of Images and Quantification of the Microarrays
[0201] After the hybridization and developing, the images of the
microarrays were identified and analysed by the ScanArray 4000
confocal fluorescent scanner (Perkin Elmer) equipped with a laser
for the green (543 nm to excite the fluorophore Cy3). The
"software" used was ScanArray 3.1. The use of the computer
programme QuantArray 3.0 (Perkin Elmer) provided the absolute
values of the intensity of hybridization and background noise in
accordance with the light emitted by the Cy3 in each probe in an
Excel format.
Data Analysis: Preliminary Processing
[0202] In first place, the value of the background noise were
subtracted from the values of absolute intensity of all the
oligonucleotides. To do this, the values of absolute intensity and
the values of background noise, which the programme used to convert
the signals of the fluorophore returns, automatically, were used
for each one of the microarray points: the corresponding in tensity
value is obtained from the zone which has been defined as point and
the value of the background noise is obtained from the zone
situated around the point.
[0203] Next, the average level of hybridization intensity of each
one of the oligonucleotides of the microarray was calculated from
the trimmed mean of the intensities of the 12 replicas of each one
of the oligonucleotides. To do this, before calculating the
average, the upper and lower values of the distribution points of
hybridization signals obtained with each one of the replicas of the
same oligonucleotide have to be eliminated. The calculation was
performed using the Excel programme from Microsoft and,
specifically, the TRIMMEAN function thereof, wherein the
"percentage" parameter was set at 0.2, which supposes fixing the
percentage of values eliminated in 20% of the upper values and 20%
of the lower values; the function rounds up the number of data
points excluded to the closest multiple of 2.
[0204] In last place, and to be able to determined the validity of
the hybridization, it is necessary that a series of established
criteria are met: 1) the ratio between the average intensity and
the aver age background of all the oligonucleotides of the chip is
greater than 10; 2) the value of the average coefficient of
variation (standard deviation of the replicas compared with the
average of the replicas) of all the replicas of oligonucleotides of
the chip should be less than 0.3; 3) the average value of the
negative control should be less than 2.5 times the value of the
DMSO medium; 4) a signal should be obtained both in the
hybridization controls and in the exogenous internal positive
controls (Spiked controls).
[0205] The data analysis was performed in R, version 1.9.1. R is a
programming language wherein both classical and modern statistical
techniques can be applied (R Developmental Core Team, 2004;
http://www.R-project.org), which has a series of functions stored
in packages for the handling, calculation and graphic
representation of data (Venables et al., 2004). There are hundreds
of packages written by different authors for R, with special
statistical functions or which permit the access and handling of
data and are available for downloading from the websites of CRAN
(http://cran.r-project.org/) or Bioconductor
(http://www.bioconductor.org). In some specific cases, the SPSS
commercial statistical analysis software was used (Chicago,
USA).
EXAMPLES
Example 1
Results Obtained on Using the Microarray Device with Samples of
U937 Vs Jurkat Cells
[0206] In order to know if the device permits differentiating two
cells lines hybridized in 10 microchips: 5 samples of biotinylated
cRNAs synthesized following the optimized working protocol,
obtained from RNA of U937 cells (cell line from promonocytic
leukemia) and 5 samples of biotinylated cRNAs obtained from RNA of
Jurkat cells (cell line from T Leukemia).
[0207] The initial steps of preliminary processing of the data and
validation of the hybridization mentioned previously in the "Data
analysis: Preliminary processing" section were carried out and then
the data was normalized and filtered: [0208] Data normalization.
The "variance stabilization normalization" method was used,
available in the "vsn" package in R. There are different packages
available on the Internet for R, with special statistical functions
or which permit the access and processing of data and are available
for downloading from CRAN (http://cran.r-project.orq/) or
Bioconductor (http://www.bioconductor.orq) [0209] ata filtering.
Two filtering operations have been carried out with the "Filterfun"
function of the of the "Genefilter" filter in R. The genes which
did not pass any of the two filters were not used in the data
analysis. The filters carried out were: [0210] Filtering to exclude
genes with an intensity value close to the DMSO. This filter made
it possible to work with genes with an intensity value minus
average background noise greater than 550 arbitrary units
(approximately 2 times the value of the DMSO). [0211] Filtering to
exclude genes with minimum intensity variation throughout the
samples. Genes were worked with an interquartile range of
normalized intensity throughout samples greater than 0.3.
[0212] The data filtering left 83 probes which constituted the
working list. With them a grouping was made of the non-supervised
samples, which are those groupings wherein the structure of the
data is not previously known, the system learning how the data are
distributed among classes based on a distance function. A tree or
hierarchical group was obtained with the grouping, wherein the
samples are grouped in accordance with their similarity in the
expression of certain genes, those corresponding to the
oligonucleotides of the working list, so that the closest samples
are those which have a similar expression profile. The grouping was
performed with the hclust function of the stats package in R. The
non-supervised analysis of the 10 samples produced their separation
in two groups or main branches in accordance with the cell type
whereto the samples belong: a group contains the 5 hybridizations
carried out from U937 cells and the other group contains the 5
hybridizations carried out from Jurkat cells. The resulting tree of
this non-supervised grouping is shown in part A of FIG. 1.
[0213] Next, to find out if there were statistically significant
differences between the two groups of samples, the "Step-down maxT
multiple testing methods" method (maxT) was used, which is an
application of the mt.maxT function of the multtest package of the
software in R from Bioconductor, which applies a statistical test
and carries out a strong control over the rate of false positives.
To this function, the following should be provided:
[0214] a) Values on which one wants to apply the statistical tests,
in this case, on the normalized values of the 83 oligonucleotides
which passed the filters
[0215] b) Groups of which one wants to seek differences, in this
case the 5 samples of Jurkat cells against the 5 samples of cells
U937
[0216] c) Number of permutations one wants to perform. In this
case, 100,000 permutations are carried out.
[0217] d) By default, Welch's test was chosen to specify the
statistical tool to be used to test the hypothesis of
non-association between the variables and the class labels.
[0218] The application of this analysis with a value of p<0.001
provided a list of 69 statistically significant probes between the
two groups, which are the following: [0219] SG12, SG20, SG23, SG24,
SG38, SG39, SG45, SG49, SG53, SG59, SG60, SG62, SG76, SG78, SG89,
SG92, SG94, SG102, SG474, SG478, SG487, SG114, SG120, SG140, SG142,
SG145, SG150, SG154, SG158, SG174, SG175, SG194, SG195, SG211,
SG230, SG231, SG235, SG260, SG264, [0220] SG266, SG268, SG270,
SG272, SG282, SG294, SG308, SG311, SG330, SG332, [0221] SG333,
SG339, SG344, SG364, SG403, SG423, SG434, SG456, SG506, SG513,
SG514, SG515, SG524, SG533, SG538, SG541, SG559
[0222] Once the statistically significant genes to distinguish
between the two groups of samples are known (which would be the
genes corresponding to the probes identified as statistically
significant) the supervised grouping was carried out of the samples
in accordance with the intensity of the signal of the 69
statistically significant probes obtained. The term "supervised",
applied to a grouping, makes reference to the fact that the data
structure is previously known, which makes it possible to use the
prior information; with this, after a training process which allows
the system to learn to distinguish between classes, it is possible
to use the network to assign new members to the predefined classes.
In this case, the supervised grouping of the samples in accordance
with the intensity of the signal obtained with the 69 statistically
significant probes obtained, is again a tree which is divided in
two main branches in accordance with the cell type to which the
samples belong. The tree obtained with the supervised grouping is
shown in part B of FIG. 1.
Example 2
Results Obtained on Using the "Array" Device with Samples from
Healthy Subjects Vs U937 and Jurkat Cells
[0223] The expression of 5 samples of U937 cells and 5 samples of
Jurkat cells was compared with the expression of 10 samples from
total blood from healthy subjects. In a manner similar to that
carried out in Example 1, the initial data processing steps,
validation of the hybridizations, normalization and filtering were
carried out. A total of 180 genes passed the filtering processes.
The non-supervised grouping of the samples (carried out with the
hclust function of the stats package of R applying Pearson's
correlation) in accordance with the expression of the 180 genes,
provided a tree with two main branches: one branch contains all the
samples from cell cultures and the other branch contains all the
samples from total blood from healthy subjects, which demonstrates
that the tool is capable of finding expression differences. The
tree obtained after making this non-supervised grouping is shown in
part A of FIG. 2.
[0224] The maxT test (p<0.001) to find genes with statistically
significant differences between the samples from U937 and Jurkart
cell cultures and the 10 samples from total blood of healthy
subjects was performed. The statistical analysis provided a list of
131 probes with statistically significant differences between both
groups of samples. They are the following:
SG1, SG4, SG7, SG8, SG10, SG13, SG15, SG16, SG17, SG18, SG19, SG20,
SG26, SG29, SG30, SG34, SG36, SG39, SG42, SG44, SG49, SG51, SG52,
SG58, SG64, SG65, SG67, SG76, SG77, SG80, SG84, SG86, SG89, SG92,
SG93, SG94, SG98, SG99, SG101, SG102, SG107, SG463, SG464, SG474,
SG475, SG485, SG487, SG466, SG467, SG471, SG472, SG473, SG120,
SG129, SG138, SG141, SG144, SG145, SG147, SG158, SG163, SG164,
SG176, SG185, SG186, SG197, SG207, SG208, SG217, SG227, SG231,
SG265, SG266, SG277, SG278, SG283, SG285, SG299, SG307, SG308,
SG311, SG313, SG318, SG319, SG328, SG333, SG336, SG342, SG344,
SG357, SG361, SG376, SG384, SG389, SG395, SG398, SG403, SG404,
SG407, SG416, SG420, SG423, SG430, SG436, SG446, SG455, SG461,
SG489, SG491, SG492, SG493, SG498, SG500, SG504, SG505, SG506,
SG514, SG516, SG517, SG520, SG526, SG530, SG533, SG538, SG545,
SG547, SG554, SG555, SG558.
[0225] The grouping of the 20 samples, in accordance with the
expression of the statistically significant probes found, gave rise
again to a tree with two main branches, one corresponding to the
samples from cell cultures and another corresponding to the samples
from healthy individuals. Said grouping appears in part B of FIG.
2.
Example 3
Results Obtained with Samples from Patients with Chronic Lymphatic
Leukemia (CLL) Vs U937 and Jurkat Cells
[0226] The expression profiles were compared of samples from U937
and Jurkats cell cultures with 26 samples from total blood of
subjects with CLL.
[0227] The samples underwent preliminary processing of the data,
they were normalized and filtered in a manner analogous to those
used in Examples 1 and 2 and a total of 236 probes passed through
the filters. The non-supervised grouping of the samples in
accordance with the expression of the probes which passed through
the filters showed a tree with two main branches: one which
contained the samples of cell cultures and the other the CLL
samples. Said tree is shown in part A of FIG. 3.
[0228] The maxT test (p<0.001) to find genes with statistically
significant differences between the two groups of samples was
carried out. This analysis provided a list of 120 probes. They are
the following: SG2, SG4, SG8, SG10, SG13, SG15, SG16, SG19, SG20,
SG23, SG26, SG28, SG31, SG34, SG36, SG39, SG48, SG58, SG60, SG65,
SG76, SG77, SG84, SG89, SG94, SG9, SG97, SG99, SG102, SG106, SG107,
SG463, SG464, SG474, SG475, SG481, SG465, SG485, SG487, SG466,
SG467, SG471, SG473, SG115, SG116, SG117, SG120, SG129, SG134,
SG135, SG138, SG139, SG141, SG145, SG158, SG161, SG163, SG176,
SG178, SG185, SG207, SG208, SG210, SG217, SG227, SG231, SG237,
SG264, SG272, SG277, SG281, SG283, SG286, SG294, SG298, SG299,
SG307, SG308, SG319, SG328, SG330, SG333, SG336, SG342, SG344,
SG345, SG347, SG361, SG384, SG389, SG395, SG404, SG407, SG416,
SG423, SG428, SG430, SG432, SG434, SG444, SG446, SG453, SG458,
SG459, SG491, SG498, SG507, SG508, SG511, SG517, SG518, SG522,
SG526, SG530, SG533, SG538, SG541, SG554, SG558, SG561.
[0229] The grouping of the 30 samples in accordance with the
expression of the 120 statistically significant probes found again
gave rise to a tree with two main branches, one corresponding to
the samples from cell cultures and another corresponding to the
samples from healthy individuals. Said grouping appears in part B
of FIG. 3.
Example 4
Results Obtained with Samples from Healthy Subjects Vs Patients
with Chronic Lymphatic Leukemia (CLL)
[0230] 68 hybridizations which met the quality criteria from 68
samples of different healthy subjects and with clinical diagnosis
of CLL were divided in 2 groups: Training Group used to obtain the
functions of the classifier and Test Group, used to test the
classifier obtained. The Training group was composed of 30 samples
(10 from healthy subjects and 20 from CLL subjects) and the Test
Group was composed of 38 samples (5 samples from healthy subjects
and 33 samples from subjects with CLL).
[0231] To obtain the classification function, the results obtained
from the hybridizations of the Training group were worked with. The
steps carried out to obtain the classification function were:
[0232] Data normalization. The "variance stabilization
normalization" method, available in the "vsn" package in R, was
used. [0233] Data filtering. Two filtering operations have been
carried out with the "Filterfun" function of thee "Genefilter"
package in R. The genes which did not pass any of the two filters
were not used in the data analysis. From the 588 oligonucleotides
of the chip, 224 passed through the 2 filters and constituted the
working list. [0234] 2. Filtering to exclude genes with an
intensity value close to the DMSO. This filter made it possible to
work with genes with an intensity value minus average background
noise greater than 550 arbitrary units (approximately 2 times the
value of the DMSO) in more than 25% of the samples (7 samples)
which compose the Training group. [0235] 3. Filtering to exclude
genes with minimum intensity variation throughout the samples.
Genes were worked with which had an interquartile range of
normalized intensity throughout samples greater than 0.3.
[0236] Two classification systems are used:
[0237] 4.1.--Construction of a Classification System with PAM.
[0238] To identify groups of genes which best characterize each
type of sample and verify the classification rate of these groups
of genes Prediction Analysis for Microarrays (PAM) was used,
available as "pamr.sup.a" package in R. It is a statistical
technique which identifies a group of genes which best
characterizes a predefined class and uses this group of genes to
predict the class whereto new samples belong. PAM uses a modified
version of the "nearest centroids" classification method
(Tibshirani et al., 2002) called "Nearest Shrunken Centroids". A
validation called "10 fold cross validation" was performed, which
consists of constructing the model with 90% of the samples and an
attempt is made to predict the class of 10% of the samples which
have not intervened in the construction of the model. This method
is repeated 10 times and the classification error of 10% of the
samples is added to calculate the overall error. This error
reflects the number of badly classified samples (Bullinger et al.,
2005).
[0239] 4.1.1. Construction of the model. From the filtered and
normalized data of the 30 samples which compose the Training group,
attributing in an arbitrary form the Healthy Group to group 0 and
the CLL Group to group 1, performing the 10 cross-validations and
with a threshold value of Delta 3.1. The model obtained was formed
by the following oligonucleotides: SG459, SG428, SG507, SG508,
SG117, SG237. The coefficients of the classifier corresponding to
each one of these oligonucleotides are shown below in Table 8:
TABLE-US-00008 TABLE 8 Coefficients of the PAM classifier id Value
0 Value 1 [1,] SG459 -0.4344 0.2172 [2,] SG428 -0.146 0.073 [3,]
SG507 -0.1111 0.0555 [4,] SG508 -0.1044 0.0522 [5,] SG117 -0.1003
0.0502 [6,] SG237 -0.0539 0.027
[0240] 4.1.2. Validation of the PAM classifier. The
cross-validation of the samples which compose the Training group
correctly classified 28 of the 30 samples.
[0241] From the filtered and normalized data of the 38 samples
which compose the Test Group, probability values p were obtained
belonging to group 0 (healthy group) or group 1 (CLL group). The
greater the value of p, the greater the probability of belonging to
that group. It has been considered that the values greater than 0.5
indicate belonging to that group. The values of p obtained for each
sample are indicated in Table 9.
TABLE-US-00009 TABLE 9 Probability values obtained with the PAM
classifier for the Test Group Sample p (Group 0) p (Group 1) S229
0.8031905 0.1968095 S231 0.7403173 0.2596827 S232 0.8810574
0.1189426 S233 0.7973159 0.2026841 S251 0.8714224 0.1285776 CLL166
0.3764637 0.6235363 CLL184 0.1278230 0.8721770 CLL132 0.2081423
0.7918577 CLL210 0.3248082 0.6751918 CLL213 0.3536033 0.6463967
CLL214 0.2705277 0.7294723 CLL221 0.3650277 0.6349723 CLL208
0.2323872 0.7676128 CLL225 0.4034316 0.5965684 CLL236 0.4893545
0.5106455 CLL240 0.3807527 0.6192473 CLL168 0.1616066 0.8383934
CLL172 0.2002317 0.7997683 CLL174 0.1601147 0.8398853 CLL175
0.6009558 0.3990442: .fwdarw.Only badly classified sample CLL177
0.1634185 0.8365815 CLL179 0.2300440 0.7699560 CLL181 0.2177406
0.7822594 CLL182 0.3450880 0.6549120 CLL164 0.2590083 0.7409917
CLL159 0.3688586 0.6311414 CLL142R 0.2111712 0.7888288 CLL105
0.2962797 0.7037203 CLL107 0.3764637 0.6235363 CLL109 0.3525788
0.6474212 CLL112 0.2059187 0.7940813 CLL151 0.2951067 0.7048933
CLL158 0.1932882 0.8067118 CLL169 0.3525937 0.6474063 CLL171
0.1495153 0.8504847 CLL178 0.2260191 0.7739809 CLL111 0.2951168
0.7048832 CLL155 0.2832151 0.7167849
[0242] With this model 37 of the 38 samples of the Test Group are
correctly classified: all the samples corresponding to healthy
individuals (those whose name is headed by the letter "S") have a
probability greater than 0.5 of belonging to group 0, whilst all
the samples corresponding to individuals suffering from CLL (which
are the samples whose name starts with letters "CLL") minus one
have a probability greater than 0.5 of belonging to group 1.
[0243] 4.2.--Construction of a Classification System with
Logistical Regression.
[0244] 4.2.1.--Selection of genes with statistically significant
differences among healthy and CLL (Training group). From the
filtered and normalized data as has been previously described, the
"Step-down maxT multiple testing methods" method (maxT) was used
for the selection of genes with significant differences, which is
an application of the mt.maxT function of the multtest package of
the software in R from Bioconductor, which applies a statistical
test and carries out a strong control over the rate of false
positives. The application of this statistical test, with a value
of p<0.001, to the 224 oligonucleotides which passed through the
filters, produced a list of 7 oligonucleotides: SG117, SG428,
SG459, SG461, SG493, SG507, SG508.
[0245] The steps used to obtain the list of 7 significant genes
among healthy and CLL were: [0246] Method which makes permutations
and adjusts the values of p resT<-mt.maxT(exprs(224
oligonucleotides which have passed through the filters and
normalized of the training group, Types of samples in the training
group, test="t", B=100000): mt.maxT function which through
permutations adjusts the probability values (signification) which
entails a strong control of the rate of false positives.
[0247] To this function the following should be provided:
1. Values on which one wants to apply the statistical tests, in
this case, on the normalized values of the 83 oligonucleotides
which passed through the filters 2. Groups of which one wants to
seek differences, in this case the 5 samples of Jurkat cells
against the 5 samples of cells U937 3. Number of permutations one
wants to perform. In this case, 100,000 permutations are carried
out. 4. By default, Welch's test was chosen as statistical
test.
[0248] The statistically significant genes at a level of p<0.001
were selected by this test and a number of 7 was obtained.
[0249] 4.2.2.--Obtainment of the classification function with SPSS.
By logistical regression from the normalized values of the 7
statistically significant oligonucleotides obtained from the 30
samples which compose the Training group and assigning in arbitrary
manner group 0 to the healthy samples and group 1 to the CLL
samples, the values of the classification function were obtained.
The coefficients corresponding to each oligonucleotide were those
which are shown below in Table 10:
TABLE-US-00010 TABLE 10 Coefficients of the classification function
Calculated by logistical regression Oligonucleotide Coefficients
(Coeff) SG117 2.44756372 SG428 7.38657611 SG459 23.1465464 SG461
43.6287742 SG493 -19.3978182 SG507 -2.80282646 SG508 49.5345672
Constant -719.241486
[0250] From these coefficients, for each sample i a value x.sub.i
is calculated as follows:
x.sub.i=Constant+(Coeff ohle0009*Imn.sub.iSG117)+(Coeff
SG428*Imn.sub.iSG428)+(Coeff SG459*Imn.sub.i SG459)+(Coeff
SG461*Imn.sub.iSG461)+(Coeff SG493*Imn.sub.i SG493)+(Coeff
SG507*Imn.sub.iSG507)+(Coeff SG508*Imn.sub.iSG508).
[0251] where Imn.sub.i is the average value of normalized intensity
of the sample i.
[0252] From the value x.sub.i a value of probability (p.sub.i) is
calculated. The closer the value of p is to 0, the greater the
probability of belonging to the group of healthy subjects (assigned
as group 0) and the closer the value of p is to 1, the greater the
probability there is of the sample belonging to the group of CLL
subjects (assigned as group 1). The formula used to determine the
value of p is:
p.sub.i=1/(1+e.sup.-xi).
[0253] As is shown in Table 11, the function obtained correctly
classified the 30 samples belonging to the training group. The
closer to 0, the greater the probability that it is healthy and the
closer to 1 the greater probability of CLL.
TABLE-US-00011 TABLE 11 Classification table.sup.a Prognosis EVOL
Correct Observed 0 1 percentage Step 1 EVOL 0 10 0 100.0 1 0 20
100.0 Overall percentage 100.0 .sup.aThe cut-off value is ,500
[0254] 4.2.3. Validation of the system classifier.--From the
filtered and normalized filters as detailed above, the Imn.sub.i
values were obtained of the 7 oligonucleotides which compose the
classifier of each one of the 38 samples which compose the Test
Group.
[0255] Results of the validation of the system classifier. Below,
tables are shown wherein the Imn.sub.i value is obtained of each
one of the 7 oligonucleotides included in the classifier and the
values of x.sub.i and p.sub.i calculated according to the formulas
previously described, obtained for each one of the 38 samples of
the Test Group. The samples which begin with S correspond to
healthy subjects and the samples which start with CLL are from CLL
subjects. 37 out of 38 samples are correctly classified. Only
sample CLL175, for which a value of pi=0 is obtained is incorrectly
classified.
TABLE-US-00012 TABLE 12 Results obtained with the Test Group by the
classification function obtained by logistical regression lmn.sub.i
S229 S231 S232 S233 S251 CLL166 CLL184 CLL132 CLL210 CLL213 CLL214
SG117 4.89 5.17 5.14 5.33 5.37 6.17 7.45 7.05 7.06 6.88 6.86 SG428
4.82 4.80 4.52 4.69 4.52 5.74 6.97 6.46 6.66 6.08 6.49 SG459 6.50
6.95 6.10 6.59 5.96 8.11 9.04 8.71 8.13 8.15 8.40 SG461 6.47 6.41
6.44 6.43 6.05 6.35 7.22 6.99 6.75 6.75 7.04 SG493 7.20 7.31 7.02
7.16 6.83 7.53 7.69 7.35 7.43 7.35 7.57 SG507 8.32 7.82 7.26 7.77
7.47 9.11 9.82 9.32 9.19 8.49 9.18 SG508 6.67 6.82 6.34 6.82 6.81
7.79 8.71 7.80 7.55 7.66 7.68 x.sub.i -71.35 -56.83 -93.68 -61.26
-86.57 17.23 129.51 70.11 33.93 38.26 55.19 p.sub.i 0.00 0.00 0.00
0.00 0.00 1.00 1.00 1.00 1.00 1.00 1.00 lmn.sub.i CLL221 CLL208
CLL225 CLL236 CLL240 CLL168 CLL172 CLL174 CLL175 CLL177 SG117 7.00
7.42 6.91 6.40 6.76 7.34 7.32 7.40 5.32 7.72 SG428 6.40 6.98 6.00
6.24 6.09 6.77 6.16 7.49 4.85 6.38 SG459 7.93 8.54 8.01 7.55 8.19
8.94 8.86 8.69 7.72 8.78 SG461 6.77 7.18 6.89 6.79 6.54 6.72 7.02
7.18 5.98 6.86 SG493 7.14 7.92 7.72 7.47 6.73 7.97 7.96 8.45 7.16
8.05 SG507 9.00 8.98 8.41 8.74 8.80 9.53 9.67 10.09 8.76 9.76 SG508
7.50 7.43 7.22 7.36 6.90 8.08 7.38 7.81 6.43 7.94 x.sub.i 31.80
50.30 12.52 8.94 3.77 67.59 39.95 63.19 -75.92 59.42 p.sub.i 1.00
1.00 1.00 1.00 0.98 1.00 1.00 1.00 0.00 1.00 lmn.sub.i CLL179
CLL181 CLL182 CLL164 CLL159 CLL142R CLL105 CLL107 CLL109 CLL112
SG117 6.89 6.92 6.14 8.03 6.98 6.80 6.52 6.17 6.79 7.31 SG428 6.32
6.22 5.64 5.40 5.55 5.94 6.05 5.74 5.81 6.52 SG459 8.52 8.71 8.35
8.54 8.00 8.87 8.32 8.11 8.20 8.77 SG461 6.83 6.95 6.87 6.96 6.63
7.07 6.72 6.35 6.66 6.80 SG493 7.99 7.92 7.71 7.73 7.49 7.96 7.79
7.53 7.70 7.99 SG507 9.40 9.53 9.37 8.86 9.34 9.49 9.49 9.11 8.89
9.41 SG508 8.17 8.18 7.37 7.80 7.81 7.97 7.75 7.79 7.46 7.69
x.sub.i 62.78 73.52 19.76 53.03 28.34 68.92 33.36 17.23 16.00 45.86
p.sub.i 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 1.00 lmn.sub.i
CLL151 CLL158 CLL169 CLL171 CLL178 CLL111 CLL155 SG117 6.51 7.26
6.79 7.76 6.62 6.51 6.90 SG428 6.14 6.17 5.81 5.96 5.97 6.14 5.44
SG459 8.40 8.81 8.20 9.18 8.77 8.40 8.44 SG461 6.64 7.01 6.66 7.10
6.79 6.64 6.71 SG493 8.00 8.12 7.70 8.03 8.05 8.00 7.91 SG507 9.11
9.36 8.89 9.52 9.36 9.11 9.35 SG508 7.87 8.29 7.46 7.99 8.06 7.87
8.23 x.sub.i 35.32 81.12 16.00 79.33 57.33 35.32 53.92 p.sub.i 1.00
1.00 1.00 1.00 1.00 1.00 1.00
[0256] A third group of 40 samples was formed. To do this, replicas
of hybridization or of labelling were used (the samples whose name
begins with S and Strans are samples from people considered healthy
and those which start with CLL are samples from patients with
chronic lymphatic leukemia). This group of samples was used to
validate the classification system. The data were normalized as has
been previously described. The results of the classification are
shown in the Table 13. 40 out of the 40 samples are correctly
classified.
TABLE-US-00013 TABLE 13 Results obtained in the validation of the
classification function obtained by logistical regression lmn.sub.i
S120.7 S120.14 Strans.3 Strans.4 S150.2 S228.6 S229.7 CLL142.8
CLL147.9 S120.7 SG117 5.22 5.40 5.41 4.95 5.47 6.05 5.34 7.06 5.39
5.22 SG428 4.95 4.64 4.29 4.20 5.01 3.89 5.07 6.31 5.59 4.95 SG459
6.39 6.14 5.46 4.98 7.14 5.72 6.23 9.01 8.56 6.39 SG461 5.73 6.16
6.23 6.38 6.72 6.01 6.39 7.02 7.05 5.73 SG493 6.78 7.05 5.03 5.15
6.95 6.37 6.22 7.87 8.07 6.78 SG507 7.83 7.62 5.83 5.78 8.17 7.26
7.85 9.74 8.82 7.83 SG508 6.42 6.46 6.90 4.56 6.62 6.70 6.71 8.19
8.17 6.42 x.sub.i -107.44 -99.01 -48.21 -172.85 -40.21 -93.50
-56.20 85.27 64.43 -107.44 p.sub.i 0.00 0.00 0.00 0.00 0.00 0.00
0.00 1.00 1.00 0.00 lmn.sub.i CLL148b.10 CLL148c.11 CLL111.12
CLL163.13 CLL108.15 CLL160.1 CLL160.2 CL L187.5 SG117 6.98 6.83
6.54 6.16 6.87 7.74 7.71 7.58 SG428 6.64 6.63 6.17 5.61 6.56 5.92
5.69 7.24 SG459 9.13 9.29 8.44 8.33 8.55 8.29 8.25 9.01 SG461 7.16
7.48 6.67 6.61 6.86 7.21 7.25 7.35 SG493 7.70 7.89 8.05 7.92 7.67
7.66 7.58 8.05 SG507 9.90 10.02 9.16 9.16 9.66 8.88 8.93 9.99 SG508
8.27 8.45 7.92 7.86 7.89 7.57 7.51 8.30 x.sub.i 102.70 125.01 39.43
28.30 58.29 51.63 48.76 109.23 p.sub.i 1.00 1.00 1.00 1.00 1.00
1.00 1.00 1.00 lmn.sub.i CLL197.14 CLL198.15 CLL199.16 CLL200.17
CLL201.18 CLL20_LE CLL208.1 CLL210.2 SG117 6.66 6.13 7.14 7.58 7.97
6.67 7.40 7.11 SG428 5.98 5.10 6.71 6.72 7.54 5.97 6.77 6.71 SG459
8.35 7.97 8.34 8.99 9.30 8.26 8.34 8.19 SG461 6.76 6.36 7.02 7.26
7.35 6.83 6.99 6.79 SG493 7.80 7.27 7.96 8.09 8.39 7.53 7.44 7.48
SG507 9.38 8.71 9.58 9.87 10.23 9.04 8.65 9.26 SG508 8.00 7.48 7.72
8.64 8.76 7.17 7.09 7.61 x.sub.i 48.40 0.40 48.33 116.75 134.69
14.31 29.64 39.38 p.sub.i 1.00 0.60 1.00 1.00 1.00 1.00 1.00 1.00
lmn.sub.i CLL225.6 CLL236.7 CLL240.8 CLL184b.9 CLL184C.10 CLL208.1
CLL213.5 CLL214.6 SG117 7.35 6.54 6.80 7.12 7.06 7.24 6.97 7.06
SG428 6.46 6.43 6.11 6.97 6.36 6.34 5.80 6.45 SG459 8.20 7.60 8.24
8.37 8.37 8.07 8.17 8.35 SG461 6.90 6.85 6.58 7.05 6.73 6.53 6.43
6.79 SG493 7.28 6.90 6.77 7.40 7.17 7.59 7.47 7.63 SG507 8.45 8.55
8.85 9.22 8.88 8.08 8.61 9.13 SG508 7.13 7.29 6.93 8.21 8.01 7.14
7.77 7.72 x.sub.i 25.36 22.47 7.52 88.13 65.29 0.80 26.04 44.00
p.sub.i 1.00 1.00 1.00 1.00 1.00 0.69 1.00 1.00 lmn.sub.i CLL221.7
CLL193.1 CLL193.2 CLL197.1 CLL197.2 SG117 6.97 6.76 6.73 6.22 6.00
SG428 6.47 7.26 7.22 5.81 5.71 SG459 7.98 8.28 8.27 8.26 8.07 SG461
6.60 7.18 7.17 6.78 6.62 SG493 7.66 7.95 7.93 7.79 7.85 SG507 9.23
9.01 9.04 8.86 8.72 SG508 7.74 7.68 7.77 7.55 7.64 x.sub.i 27.46
56.71 60.37 23.63 14.87 p.sub.i 1.00 1.00 1.00 1.00 1.00
Example 5
Results Obtained with "Stable" CLL Samples Compared with
"Progressive" CLL Samples
[0257] "CLL-stable type" (S) samples are considered those of
patients who have had stable CLL for over 5 years and
"CLL-progressive type" (P) samples are considered the samples of
patients classified as stable at the time of diagnosis and whose
disease has progressed in less than one year.
[0258] In total 6 S samples and 6 P samples were analysed. The 12
samples were collected at the time of diagnosis, without clinical
differences between them, but after one year, 6 of those patients
had progressed. The 12 hybridizations have passed the
aforementioned quality criteria.
[0259] Stable samples: E142R, E148, E156, E163, E164, E193
[0260] Progressive samples: P111, P105, P177, P158, P157 and
P197.
[0261] All the data analysis was performed in R version 1.9.1.
[0262] Data normalization. In this case, and to avoid the
significant genes obtained are due to a real difference between
samples and not to the effect of normalization, the data were
normalized in two different forms ("variance stabilization
normalization" (vsn) and by robust quantiles) and the same
statistical analysis was performed with each one of the
normalizations. [0263] Statistical analysis with normalized data by
"variance stabilization normalization". The list of statistically
significant genes was obtained from a Welch's test with the mt.maxT
function of the multtest package in R, with a value of p<0.05
without adjusting, i.e. without performing any control on the false
positives and produced a list of 29 genes with stat istically
significant differences between the CLL-stable type and
CLL-progressive type groups.
[0264] The statistically significant oligonucleotides obtained
were:
SG26, SG31, SG70, SG98, SG177, SG194, SG195, SG208, SG213, SG216,
SG272, SG293, SG301, SG309, SG321, SG333, SG343, SG352, SG357,
SG366, SG368, SG405, SG426, SG439, SG447, SG452, SG521, SG555,
SG556.
[0265] The samples were grouped, which was performed with the
hclust function of the stats package in R applying Pearson
correlations. The tree obtained is shown in part A of FIG. 4.
[0266] The hierarchical grouping of the 12 samples in accordance
with the expression of the 29 statistically significant genes
obtained grouped the samples correctly: the tree contains two large
branches, of which the right branch contains the 6 stable samples
and the left branch contains the 6 progressive samples. [0267]
Statistical analysis with normalized data by robust quantiles The
list of statistically significant genes was obtained from a Welch's
test with the mt.maxT function of the multtest package in R with
the values of p without adjusting i.e. without exerting any control
over the rate of false positives, with a value of p<0.05, and
produced a list of 19 genes with statistically significant
differences between the CLL-stable type and CLL-progressive type
groups: [0268] SG26, SG31, SG177, SG194, SG195, SG197, SG213,
SG216, SG293, SG301, SG309, SG333, SG343, SG357, SG366, SG439,
SG452, SG555, SG556.
[0269] The supervised grouping of the 12 samples in accordance with
the expression of the 19 statistically significant genes obtained
gave rise to the tree which appears in part B of FIG. 4, wherein
the samples also appear correctly grouped.
[0270] 18 oligonucleotides common to both lists of statistically
significant genes were selected and the average intensity of each
one of them in the group of stable samples and in the group of
progressive samples was calculated, as well as the variation in
average intensity between the stable and progressive groups.
[0271] The values obtained are shown in Table 14.
TABLE-US-00014 TABLE 14 Values corresponding to the intensity of 18
significant oligonucleotides to distinguish between CLL-stable and
CLL-progressive Stable CLL Progressive CLL Change group group
stable/ Significance Average Average progres- Probe (p data vsn)
Intensity SD Intensity SD sive SG177 0.001 14 1.71 21 4.84 0.7
SG366 0.001 18 2.33 14 1.80 1.3 SG309 0.004 20 2.76 15 3.58 1.4
SG26 0.005 97 19.20 70, 13.24 1.4 SG452 0.010 16 2.19 12 3.08 1.3
SG216 0.012 46 14.64 31 7.13 1.5 SG333 0.013 36 7.28 53 16.25 0.7
SG357 0.014 134 6.50 175 38.67 0.8 SG213 0.014 26 5.51 41 17.20 0.6
SG31 0.014 69 32.50 30 10.57 1.8 SG301 0.014 21 5.02 16 3.10 1.4
SG194 0.019 37 9.52 50 9.95 0.7 SG456 0.022 11 2.06 14 2.08 0.8
SG293 0.029 17 1.88 21 3.72 0.8 SG343 0.033 27 7.43 21 1.61 1.3
SG439 0.038 18 2.00 20 1.74 0.9 SG195 0.041 21 3.56 25, 4.60 0.8
SG555 0.049 163 23.55 137 20.69 1.2
[0272] To validate the results obtained with the microarray, 5 of
the common statistically significant probes were selected obtained
on comparing expression data from stable CLL subjects compared to
progressive CLL subjects and the expression was studied with RT-PCR
of the genes represented by those probes. The criteria used to
select the 5 probes were: hybridization intensity, change of
intensity between groups of stable and progressive and value of
statistical significance. In this way, 5 probes were selected which
represent genes PSMB4, CD23A, LCP1, ABCC5 and POU2F2. The
expression of these 5 genes was determined in 11 of the 12 CLL type
samples, as there was no total RNA of sample 105. With the
expression value of the genes in each sample, the rate of change
was determined between the group of stable and progressive and the
value of significance of that variation and it was compared with
the results obtained with the microarrays.
[0273] The technique used for the validation was RT-PCR or PCR in
real time using a LightCycler. This technique is the technique of
choice to validate data chips and as with the microarrays, measures
mRNA level.
[0274] Primers were designed for each one of the 5 genes whose
representative oligonucleotide was selected. The details thereof
are shown below in Table 15.
TABLE-US-00015 TABLE 15 Primers and amplification products of the
genes selected for their validation by RT-PCR Amplified product
Gene Primer sequences (5'-3') SEQ ID NO: size T.sub.m PSMB4 Direct:
PSMB4_F SEQ ID NO: 598 95 pb 81.degree. C. TTCTGGGAGATGGACACAGCTATA
Inverse: PSMB4_R SEQ ID NO: 599 CCACAAAGGGTTCATCTTCGA CD23A Direct:
CD23A_F SEQ ID NO: 600 97 pb 82.degree. C. TGCCCTGAAAAGTGGATCAAT
Reverse: CD23A_R SEQ ID NO: 601 CCATGTCGTCACAGGCATACC LCP1 Direct:
LCP1_F SEQ ID NO: 602 126 pb 77.degree. C. CCAGGTACCCTTCTCGCTTTT
Reverse: LCP1_R SEQ ID NO: 603 CTCCTGGCCCTCATCTTGAA ABCC5 Direct:
ABCC5_F SEQ ID NO: 604 119 pb 82.degree. C.
CCCTCAAAGTCTGCAACTTTAAGC Reverse: ABCC5_R SEQ ID NO: 605
ACACACCAAACCACACAGCAA POU2F2 Direct: POU2F2_F SEQ ID NO: 606 136 pb
82.degree. C. GAGGACCAGCATCGAGACAAA Reverse: POU2F2_R SEQ ID NO:
607 AACCAGACGCGGATCACTTC
[0275] FIG. 5 shows the distribution of the expression data
obtained by RT-PCR (left graphic) and by the microarray (right
graphic). Part A corresponds to gene PSMB4, part B to gene CD23A
and part C to gene POU2F2.
[0276] Below, in Table 16, the results obtained with the microarray
and with RT-PCR are obtained of the change values of the 5 genes
selected in thr group of stable samples compared with the group of
progressive samples obtained as significance of the change. In 3 of
the 5 genes selected (PSMB4, CD23A and POU2F2) the values of
change, the direction of the change and the significance values
obtained with RT-PCR agree with those obtained with the microarray,
for which reason those 3 genes are considered valid, i.e. the
results obtained for those 3 genes with the microarray coincide
with the results obtained by another techniques which also measures
mRNA level.
TABLE-US-00016 TABLE 16 Values of change and significance of the
change obtained with the microarray and by RT-PCR
Stable/progressive change Significance of the change Probes Genes
Array RT-PCR Array RT-PCR SG26 PSBM4 1.3 1.5 0.04 0.15 SG216 CD23A
1.5 3.2 0.04 0.03 SG333 LCP1 0.7 1 0.05 0.97 SG357 ABCC5 0.8 1.3
0.10 0.28 SG366 POU2F2 1.3 2.3 0.01 0.05
BIBLIOGRAPHIC REFERENCES
[0277] Alizadeh A, Eisen M, Davis R E, et al The lymphochip: a
specialized cDNA microarray for the genomic-scale analysis of gene
expression in normal and malignant lymphocytes. Cold Spring Harb
Symp Quant Biol. 1999; 64:71-8. [0278] Alizadeh A A, Eisen M B,
Davis R E, et al Distinct types of diffuse large B-cell lymphoma
identified by gene expression profiling. Nature. 2000; 403:503-11.
[0279] Arico M, Valsecchi M G, Camitta B, Schrappe M, Chessells J,
Baruchel A, Gaynon P, Silverman L, Janka-Schaub G, Kamps W, Pui C
H, Masera G. Outcome of treatment in children with Philadelphia
chromosome-positive acute lymphoblastic leukemia N Engl J. Med.
2000; 342:998-1006.). [0280] Bea S, Zettl A, Wright G, et al.
Diffuse Large B-Cell Lymphoma Subgroups Have Distinct Genetic
Profiles that Influence Tumor Biology and Improve Gene
Expression-Based Survival Prediction. Blood. 2005 04:-1399 [0281]
Bene M C, Bernier M, Casasnovas R O, et al: Acute myeloid leukaemia
M O: Haematological, immunophenotypic and cytogenetic
characteristics and their prognostic significance: An analysis in
241 patients. Br J Haemat 113:737, 2001.
[0282] Benes V, Muckenthaler M. Standardization of protocols in
cDNA microarray analysis. Trends Biochem Sci. 2003; 28:244-9 [0283]
Bennett J M, Catovsky D, Daniel M T, et al. Myelodysplastic
syndromes: is another classification necessary? Br J. Haematol.
1984; 56:515-7. [0284] Bennett J M, Catovsky D, Daniel M T, et al.
Proposals for the classification of the acute leukaemias.
French-American-British (FAB) co-operative group. Br J. Haematol.
1976; 33:451-8. [0285] Bergh G, Ehinger M, Olsson I, Jacobsen S E,
Gullberg U. Involvement of the retinoblastoma protein in monocytic
and neutrophilic lineage commitment of human bone marrow progenitor
cells Blood. 1999; 94:1971-8 [0286] Bernard J, Levy J P, Varet B.
Hematologie. Collection Medico Chirurgicale. Paris: Flammarion,
1976; 5-22 [0287] Binet J L, Auquier A, Dighiero G, et al. A new
prognostic classification of chronic lymphocytic leukemia derived
from a multivariate survival analysis. Cancer. 1981; 48:198-206
[0288] Boultwood J, Lewis S, Wainscoat J S The 5q-syndrome. Blood.
1994; 84:3253-60 [0289] Braziel R M, Shipp M A, Feldman A L, et al.
Molecular diagnostics. Hematology (Am Soc Hematol Educ Program).
2003; 279-93 [0290] Bullinger, Milner et al. Use of gene-expression
profiling to identify prognostic subclasses in adult acute myeloid
leukemia N Engl Med 2005; 350:1605-16 [0291] Chan W C. Gene
expression profiling in lymphoma diagnosis and research. Croat Med
J. 2005; 46:349-59 [0292] Chen C C, Andrich M P, Metcalfe D D: A
retrospective analysis of bone scan abnormalities in mastocytosis:
Correlation with disease category and prognosis. J Nucl Med
35:1471, 1994 [0293] Cossman J: Gene expression analysis of single
neoplastic cells and the pathogenesis of Hodgkin's lymphoma. J
Histochem Cytochem 2001; 49:799-800 [0294] Crespo M, Bosch F,
Villamor N, et al. ZAP-70 expression as a surrogate for
immunoglobulin-variable-region mutations in chronic lymphocytic
leukemia. N Engl J. Med. 2003; 348:1764-75 [0295] Datta S R, Brunet
A, Greenberg M E. Cellular survival: A play in three acts. Genes
Dev 1999; 13: 2905-2927 [0296] Devilard E, Bertucci F, Tremat P, et
al: Gene expression profiling defines molecular subtypes of
classical Hodgkin's lymphoma. Oncogene 2002; 21:3095-3102 [0297]
Dohner K, Tobis K, Ulrich R, Frohling S, Benner A, Schlenk R F,
Dohner H. Prognostic significance of partial tandem duplications of
the MLL gene in adult patients 16 to 60 years old with acute
myeloid leukemia and normal cytogenetics: a study of the Acute
Myeloid Leukemia Study Group Ulm. J Clin Oncol. 2002; 20:3254-61
[0298] Domen J, Weissman I L. Self-renewal, differentiation or
death: regulation and manipulation of hematopoietic stem cell fate.
Mol Med. Today. 1999; 5:201-8 [0299] Durig J, Naschar M, Schmucker
U, Renzing-Kohler K, Holter T, Huttmann A, Duhrsen U. CD38
expression is an important prognostic marker in chronic lymphocytic
leukaemia. Leukemia. 2002; 16:30-5 [0300] Ferrando A A, Look A T
Pathobiology of acute lymphoblastic leukemia. In Hoffman R
Hematology Basic Principles and practice. 4 ed. Churchill
Livingstone New York 2005; 1135-1147 [0301] Galton D A. The
pathogenesis of chronic lymphocytic leukemia Can Med Assoc J. 1966;
94:1005-10 [0302] Giles F J, Keating A, Goldstone A H, Avivi I,
Willman C L, Kantarjian H M Acute myeloid leukemia. Hematology (Am
Soc Hematol Educ Program). 2002; 73-110.). [0303] Golub T R, Slonim
D K, Tamayo P, et al. Molecular classification of cancer: class
discovery and class prediction by gene expression monitoring.
Science. 1999; 286:531-7 [0304] Gong J Z, Lagoo A S, Peters D,
Horvatinovich J, Benz P, Buckley P J. Value of CD23 determination
by flow cytometry in differentiating mantle cell lymphoma from
chronic lymphocytic leukemia/small lymphocytic lymphoma Am J Clin
Pathol. 2001; 116:893-7 [0305] Greiner TC.mRNA microarray analysis
in lymphoma and leukemia. Cancer Treat Res. 2004; 121:1-12 [0306]
Guttmacher A E, Collins F S. Welcome to the genomic era N Engl J.
Med. 2003; 349:996-8 [0307] Hamblin T J, Davis Z, Gardiner A,
Oscier D G, Stevenson F K Unmutated Ig V(H) genes are associated
with a more aggressive form of chronic lymphocytic leukemia. Blood.
1999; 94:1848-54 [0308] Hanahan D, Weinberg R A: The hallmarks of
cancer. Cell 100:57-70, 2000 [0309] Harris N L, Jaffe E S, Diebold
J, et al. The World Health Organization classification of
neoplastic diseases of the hematopoietic and lymphoid tissues.
Report of the Clinical Advisory Committee meeting, Airlie House,
Virginia, November, 1997 Ann Oncol. 1999; 10:1419-32 [0310] Harris
N L, Jaffe E S, Diebold J, et al. World Health Organization
classification of neoplastic diseases of the hematopoietic and
lymphoid tissues: report of the Clinical Advisory Committee
meeting, Airlie House, Virginia, November 1997 J Clin Oncol. 1999;
17:3835-49 [0311] Harris N L, Jaffe E S, Stein H, et al A revised
European-American classification of lymphoid neoplasms: a proposal
from the International Lymphoma Study Group Blood. 1994; 84:1361-92
[0312] Harris N L, Stein H, Coupland S E, Hummel M, Favera R D,
Pasqualucci L, Chan W C New approaches to lymphoma diagnosis.
Hematology (Am Soc Hematol Educ Program). 2001; 194-220. [0313]
Heaney M L, Golde D W Myelodysplasia. N Engl J. Med. 1999;
340:1649-60 [0314] Jaffe E S, Harris N L, Stein H, Vardiman J W.
WHO Classification Tumours of Heamotopoietic and lymphoid tissues.
En Pathology and Genetics of tumours of Haematopoietic and lymphoid
tissues. IARC Press. Lyon, 2001. [0315] Jemal A, Murray T, Samuels
A, et al: Cancer statistics, 2003. CA Cancer J Clin 53:5, 2003
[0316] Kottaridis P D, Gale R E, Frew M E, et al. The presence of a
FLT3 internal tandem duplication in patients with acute myeloid
leukemia (AML) adds important prognostic information to cytogenetic
risk group and response to the first cycle of chemotherapy:
analysis of 854 patients from the United Kingdom Medical Research
Council AML 10 and 12 trials. Blood. 2001; 98:1752-9 [0317] Kuppers
R, Klein U, Hansmann M L, Rajewsky K. Cellular origin of human
B-cell lymphomas. N Engl J. Med. 1999; 341:1520-9 [0318] Kuppers R:
Molecular biology of Hodgkin's lymphoma. Adv Cancer Res 2002;
84:277-312 [0319] Kyle R A: Monoclonal gammopathy of undetermined
significance and solitary plasmacytoma: Implications for
progression to overt multiple myeloma. Hematol Oncol Clin North Am
11:71, 1997 [0320] Lee M F, Dang C V Control of cell division. In
Hoffman R Hematology Basic Principles and practice. 4 ed. Churchill
Livingstone New York 2005; 69-81 [0321] Leung AYH, Verfaillie C M
Stem cell model of hematopoyesis. In Hoffman R Hematology Basic
Principles and practice. 4 ed. Churchill Livingstone New York 2005;
200-214 [0322] Magli M C, Largman C, Lawrence H J Effects of HOX
homeobox genes in blood cell differentiation J Cell Physiol. 1997;
173:168-77 [0323] Mitelman F, Mertens F, Johansson B A breakpoint
map of recurrent chromosomal rearrangements in human neoplasia.
Nat. Genet. 1997; 15 Spec No:417-74 [0324] Montoto S,
Lopez-Guillermo A, Colomer D, et al. Incidence and clinical
significance of bcl-2/IgH rearrangements in follicular lymphoma.
Leuk Lymphoma. 2003; 44:71-6. [0325] Nichogiannopoulou A, Trevisan
M, Friedrich C, Georgopoulos K. Ikaros in hemopoietic lineage
determination and homeostasis Semin Immunol. 1998; 10:119-25.
[0326] Nutt S L, Heavey B, Rolink A G, Busslinger M. Commitment to
the B-lymphoid lineage depends on the transcription factor Pax5.
Nature. 1999; 401:556-62 [0327] O'Gorman D M, Cotter T G Molecular
signals in anti-apoptotic survival pathways. Leukemia. 2001;
15:21-34 [0328] Pane F, Intrieri M, Quintarelli C, Izzo B, Muccioli
G C, Salvatore F BCR/ABL genes and leukemic phenotype: from
molecular mechanisms to clinical correlations. Oncogene. 2002;
21:8652-67. [0329] R Development Core Team. R: A language and
environment for statistical computing. R Foundation for Statistical
Computing, Vienna, Austria, 2004 [0330] Rai K R, Sawitsky A,
Cronkite E P, Chanana A D, Levy R N, Pasternack B S. Clinical
staging of chronic lymphocytic leukemia. Blood. 1975; 46:219-34
[0331] Roumier C, Eclache V, Imbert M, et al. M O AML, clinical and
biologic features of the disease, including AML1 gene mutations: A
report of 59 cases by the Groupe Francais d'Hematologie Cellulaire
(GFHC) and the Groupe Francais de Bytogenetique Hematologique
(GFCH). Blood 101:1277, 2003 [0332] Shaffer A L, Rosenwald A,
Staudt L M Lymphoid malignancies: the dark side of B-cell
differentiation Nat Rev Immunol. 2002; 2:920-32 [0333] Tenen D G,
Hromas R, Licht J D, Zhang D E Transcription factors, normal
myeloid development, and leucemia. Blood. 1997; 90:489-519 [0334]
Tibshirani R, Hastie T, Narasimhan B, Chu G. Diagnosis of multiple
cancer types by shrunken centroids of gene expression. Proc. Natl.
Acad. Sci. 2002; 99:6567-72 [0335] Vardiman J W, Harris N L,
Brunning R D The World Health Organization (WHO) classification of
the myeloid neoplasms. Blood. 2002; 100:2292-302 [0336] Venables,
Smith et al. An Introduction to R, Notes on R: A programming
Environment for Data Analysis. 2004 [0337] Weissman I L Stem cells:
Units of regeneration and units in evolution. Cell, 2000;
100:157-168. [0338] Westbrook C A. The molecular basis of
neoplasia. In Hoffman R Hematology Basic Principles and practice. 4
ed. Churchill Livingstone New York 2005; 941-945 [0339] Zhan F,
Hardin J, Kordsmeier B, et al: Global gene expression profiling of
multiple myeloma, monoclonal gammopathy of undetermined
significance, and normal bone marrow plasma cells. Blood 99:1745,
2002
BRIEF DESCRIPTION OF THE FIGURES
[0340] FIG. 1 shows the grouping of samples of cells U937 compared
with Jurkat cells in accordance with differences in the gene
expression between the samples. Part A corresponds to the
non-supervised grouping; part B corresponds to the supervised
grouping.
[0341] FIG. 2 shows the grouping of samples of healthy subjects
compared with U937 and Jurkat cells in accordance with differences
in the gene expression between the samples. Part A corresponds to
the non-supervised grouping; part B corresponds to the supervised
grouping.
[0342] FIG. 3 shows the grouping of samples of patients with
chronic lymphatic leukemia compared with U937 and Jurkat cells in
accordance with differences in the gene expression between the
samples. Part A corresponds to the non-supervised grouping; part B
corresponds to the supervised grouping.
[0343] FIG. 4 shows the grouping of samples of patients with
"stable" chronic lymphatic leukemia compared with samples of
patients with "progressive" chronic lymphatic leukemia in
accordance with differences in gene expression. Part A corresponds
to the grouping in accordance with the genes identified as
significant after normalization with "vsn" and use of the mt.maxT
function in R; part B corresponds to the grouping in accordance
with the genes identified as significant after normalization by
robust quartiles and use of the mt.maxT function in R.
[0344] FIG. 5 shows the distribution of the expression data
obtained by RT-PCR (left-hand graphic) and from the intensity
values obtained from the microarray (right-hand graphic) for the
PSMB4 genes (part A: upper graphic), CD23A (part B: intermediate
graphic) and POU2F2 (part C: lower graphics) in samples of patients
with "stable" chronic lymphatic leukemia (bars marked with "E") and
in samples of patients with "progressive" chronic lymphatic
leukemia (bars marked with "P").
Sequence CWU 1
1
607150DNAArtificial SequenceProbe SG1 designed to hybridize with
cRNA of the human gene GABARAP 1tccagtgatt gttttggttt ctgttccctt
tctgactgcc caaggggctc 50250DNAArtificial SequenceProbe SG2 designed
to hybridize with cRNA of the human gene IGLV6-57 2ttatgatagc
acctatcatg tgatattcgg cggagggacc aagctgaccg 50355DNAArtificial
SequenceProbe SG3 designed to hybridize with cRNA of the human gene
PCD 3gccgtctctt gctccctaat tcatttccca ggaagctgtg atacagggtg aaata
55453DNAArtificial SequenceProbe SG4 designed to hybridize with
cRNA of the human gene NCALD 4ccactgaccc tgtctgtatt ttctcggagg
ttgtttttct ccttctcctt ccc 53555DNAArtificial SequenceProbe SG5
designed to hybridize with cRNA of the human gene DLAD 5gagtccacac
caagccttca gaagtggagg attcatttgt acccagaatt ggcaa
55655DNAArtificial SequenceProbe SG6 designed to hybridize with
cRNA of the human gene SOSTDC1 6cgcttggaat ggaatgccag aaatgcatgg
cagcagctaa taagtaaagc tgatt 55755DNAArtificial SequenceProbe SG7
designed to hybridize with cRNA of the human gene T1A-2 7ggaaagaccg
ttcaccagac ttggctcctc taaacatttg ctgttcaaac atgtt
55855DNAArtificial SequenceProbe SG8 designed to hybridize with
cRNA of the human gene PYGB 8ccctgaccac cactgtgccc ctcattgtta
ctgccttgtg agataaaaac tgatt 55951DNAArtificial SequenceProbe SG9
designed to hybridize with cRNA of the human gene LIMS1 9atgggcaagc
agtggcatgt ggagcatttt gtttgtgcca agtgtgagaa a 511051DNAArtificial
SequenceProbe SG10 designed to hybridize with cRNA of the human
gene ABL1 10atccaaatct gtcctcgtcc tccagctgtt atctggaaga agcccttcag
c 511150DNAArtificial SequenceProbe SG11 designed to hybridize with
cRNA of the human gene DRG1 11attgtgaaga agtgaaacct ttcccttttc
ccatctgccg gacgaaccac 501250DNAArtificial SequenceProbe SG12
designed to hybridize with cRNA of the human gene BRMS1
12agaagacagc cgaagtcaaa gccacatcct cttgctgatg ttggatgcag
501355DNAArtificial SequenceProbe SG13 designed to hybridize with
cRNA of the human gene ABHD1 13gaggacagaa acagctgaca agagtaccat
ttggggtctc agttcactct ttcct 551455DNAArtificial SequenceProbe SG14
designed to hybridize with cRNAof the human gene IFRD1 14tgaattcctt
cgaaatgtat ttgaacttgg acccccagtg atgcttgatg ctgca
551555DNAArtificial SequenceProbe SG15 designed to hybridize with
cRNA of the human gene RPL36A 15cgttgagccc aactgcagat ctaagagaat
gctggctatt aaaagatgca agcat 551650DNAArtificial SequenceProbe SG16
designed to hybridize with cRNA of the human gene IGFBP2
16agttctgaca cacgtattta tatttggaaa gagaccagca ccgagctcgg
501750DNAArtificial SequenceProbe SG17 of designed to hybridize
with cRNA the human gene NDRG1 17gactttcctt ccctctcctg cttcctcttt
tcctgctccc taacctttcg 501855DNAArtificial SequenceProbe SG18
designed to hybridize with cRNA of the human gene FKBP9
18cgtgactcac catgcccagc cacttagttt tttcttattc ccacctttct atccc
551950DNAArtificial SequenceProbe SG19 designed to hybridize with
cRNA of the human gene NDP52 19tttttttttt gaaacagtct ctctctgtca
cccaggctgg cgtgcaatgg 502055DNAArtificial SequenceProbe SG20
designed to hybridize with cRNA of the human gene FABP5
20ggtgcattgg ttcagcatca ggagtgggat gggaaggaaa gcacaataac aagaa
552155DNAArtificial SequenceProbe SG21 designed to hybridize with
cRNA of the human gene FARP1 21acggtttcca gtactaacaa agggaataaa
aatacctcac gccacaatcc agcat 552246DNAArtificial SequenceProbe SG22
designed to hybridize with cRNA of the human gene PGF 22ggaagaggag
gagagagaag cagagaccca cagactgcca cctgtg 462355DNAArtificial
SequenceProbe SG23 designed to hybridize with cRNA of the human
gene GDI2 23gcctgagaag gaaatcagac cagctttgga gctcttggaa ccaattgaac
agaaa 552455DNAArtificial SequenceProbe SG24 designed to hybridize
with cRNA of the human gene TAGLN2 24gagggctgcc taccatggtc
tggggcttga ggaagatgag tttgttgatt taaat 552555DNAArtificial
SequenceProbe SG25 designed to hybridize with cRNA of the human
gene BLVRB 25ggacatgagg agcaaaggaa gggggcaata aatgttgagc caagagcttc
aaatt 552650DNAArtificial SequenceProbe SG26 designed to hybridize
with cRNA of the human gene PSMB4 26ttacaaccgg tttcaaaccg
ccactgtcac cgaaaaaggt gttgaaatag 502750DNAArtificial SequenceProbe
SG27 designed to hybridize with cRNA of the human gene TACSTD2
27gaccacatat gcttgtcact gggaaagaag cctgtttcag ctgcctgaac
502850DNAArtificial SequenceProbe SG28 designed to hybridize with
cRNA of the human gene TCEB1 28acaaggttcg ctacactaac agctccaccg
agattcctga attcccaatt 502955DNAArtificial SequenceProbe SG29
designed to hybridize with cRNA of the human gene EEF1A1
29gagaatgttt tgtggacacg ttggttttct tttttgcgtg tggcagtttt agtta
553055DNAArtificial SequenceProbe SG30 designed to hybridize with
cRNA of the human gene H3F3A 30ccgcatacgt ggagaacgtg cttaagaatc
cactatgatg ggaaacattt cattc 553155DNAArtificial SequenceProbe SG31
designed to hybridize with cRNA of the human gene ODC1 31gcatttgtag
cttgtacaat ggcagaatgg gccaaaagct tagtgttgtg acctg
553255DNAArtificial SequenceProbe SG32 designed to hybridize with
cRNA of the human gene XRCC5 32cccagtcacc tctgtcttca gcaccctcat
aagtcgtcac taatacacag ttttg 553350DNAArtificial SequenceProbe SG33
designed to hybridize with cRNA of the human gene IGFBP3
33ttcacttctc tgtcttctgt ttctctccca cagtgtcgcc cttccaaagg
503451DNAArtificial SequenceProbe SG34 designed to hybridize with
cRNA of the human gene NCL 34aggaggagga ggtgaccaca agccacaagg
aaagaagacg aagtttgaat a 513555DNAArtificial SequenceProbe SG35 cRNA
designed to hybridize with cRNA of the human gene S100A2
35ctgccatgga tctcttgggc ccaggactgt tgatgccttt gagttttgta ttcaa
553653DNAArtificial SequenceProbe SG36 designed to hybridize with
cRNA of the human gene RPL24 36tcagctcccc gagttggtgg aaaacgctaa
actggcagat tagattttta aat 533755DNAArtificial SequenceProbe SG37
designed to hybridize with cRNA of the human gene GJA1 37cacccctaag
aatggttctg tgtatgtgaa tgagcgggtg gtaattgtgg ctaaa
553850DNAArtificial SequenceProbe SG38 designed to hybridize with
cRNA of the human gene GUSB 38aatgtttgga aaacagcccg tttacttgag
caagactgat accacctgcg 503955DNAArtificial SequenceProbe SG39
designed to hybridize with cRNA of the human gene HSD17B1
39gttggagacc agccagagca acacagtgag acccccatct ctacaaaaat aaaga
554050DNAArtificial SequenceProbe SG40 designed to hybridize with
cRNA of the human gene SFTPB 40ttttcaaaaa atcagcaatt ccccagcgta
gtcaagggtg gacactgcac 504150DNAArtificial SequenceProbe SG41
designed to hybridize with cRNA of the human gene RPL23A
41attcggcctg atggagagaa gaaggcatat gttcgactgg ctcctgatta
504255DNAArtificial SequenceProbe SG42 designed to hybridize with
cRNA of the human gene CSRP2 42ggctaactcg taggaagaga gcactgtatg
gtatcctttt gctttattca ccagc 554355DNAArtificial SequenceProbe SG43
designed to hybridize with cRNA of the human gene CXADR
43tgctgttgtg tgatcaaaca tgtctctgtg tagttccagc aaatcaagct gagct
554450DNAArtificial SequenceProbe SG49 designed to hybridize with
cRNA of the human gene EEF1G 44tttggaacca acaatagcag ctccatttct
ggagtctggg tcttccgagg 504554DNAArtificial SequenceProbe SG45
designed to hybridize with cRNA of the human gene CKS2 45tgcatgagct
gtattcttca cagcaacaga gctcagttaa atgcaactgc aagt
544651DNAArtificial SequenceProbe SG46 designed to hybridize with
cRNA of the human gene COL4A6 46attaatggca tatggtccta gacaaaccat
ctcctccttg ccggctcccc c 514755DNAArtificial SequenceProbe SG47
designed to hybridize with cRNA of the human gene CRYAB
47gctgtcaccg cagcccccaa gaaatagatg ccctttcttg aattgcattt tttaa
554855DNAArtificial SequenceProbe SG48 designed to hybridize with
cRNA of the human gene CYC1 48gctctagctc tgggccctcc ttcagccccc
atcatgggaa taaattaatt ttctc 554950DNAArtificial SequenceProbe SG49
designed to hybridize with cRNA of the human gene FNTB 49tcactcctcc
ctatcatgta ccgtgaaaac cccctctgat ggcctcaagg 505050DNAArtificial
SequenceProbe SG50 designed to hybridize with cRNA of the human
gene GOT1 50aaagatcaag ttgtctgaag gagccaaagt gtgaatgtgg gtgtcggctg
505146DNAArtificial SequenceProbe SG51 designed to hybridize with
cRNA of the human gene LGALS7 51cttggttcct cccaatgcca gcaggttcca
tgtaaacctg ctgtgc 465250DNAArtificial SequenceProbe SG52 designed
to hybridize with cRNA of the human gene SERPINB5 52ttgatagctg
tcccatctgg tcatgtggtt ggcactagac tggtggcagg 505350DNAArtificial
SequenceProbe SG53 designed to hybridize with cRNA of the human
gene PSMC5 53agaaaaattg ctgagctcat gccaggagca tcaggggctg aagtgaaggg
505455DNAArtificial SequenceProbe SG54 designed to hybridize with
cRNA of the human gene PTN 54ccctgtggca aactgaccaa gcccaaacct
caagcagaat ctaagaagaa gaaaa 555555DNAArtificial SequenceProbe SG55
designed to hybridize with cRNA of the human gene RBBP8
55ggcaaggagc agaagacata gacgttgaaa cagaaacaga aggatgaagg acagt
555655DNAArtificial SequenceProbe SG56 designed to hybridize with
cRNA of the human gene RGS1 56gcccctcaga actgggaagg ccaggtaact
ctagttacac agaaactgtg actaa 555750DNAArtificial SequenceProbe SG57
designed to hybridize with cRNA of the human gene RXRA 57tttcgagtaa
tttttaaagc cttgctctgt tgtgtcctgt tgccggctct 505854DNAArtificial
SequenceProbe SG58 designed to hybridize with cRNA of the human
gene SDHD 58gcttggagtg cttctgaata tacagaagtt ccatttaagg gcaagtttcc
ccgt 545950DNAArtificial SequenceProbe SG59 designed to hybridize
with cRNA of the human gene SEPW1 59tctcaagggg aagccaagag
aggcatcagg atgggtgggt ttctgattgt 506055DNAArtificial SequenceProbe
SG60 designed to hybridize with cRNA of the human gene SSBP1
60gccaggcctc agagacgtgg catatcaata tgtgaaaaag gggtctcgaa tttat
556155DNAArtificial SequenceProbe SG61 designed to hybridize with
cRNA of the human gene TEGT 61acgaaatcat ttgtttctaa gttgtgttta
ttcctggagt gacatgccac cccga 556250DNAArtificial SequenceProbe SG62
designed to hybridize with cRNA of the human gene HIST1H2BN
62tctcgtccaa ggccatgggc atcatgaact ccttcgtcaa tgacatcttc
506355DNAArtificial SequenceProbe SG63 designed to hybridize with
cRNA of the human gene BECN1 63ccagccctgg tcagttttga ttcttaaccc
catggactcc tttccctttc ttctc 556455DNAArtificial SequenceProbe SG64
designed to hybridize with cRNA of the human gene ANXA7
64gtcaaggacc gtatcagggt aatgtgcttg gtttgcacat gttgttattg cctta
556555DNAArtificial SequenceProbe SG65 designed to hybridize with
cRNA of the human gene NDUFA1 65gcgcatctct ggagttgatc gttactatgt
gtcaaagggt ttggagaaca ttgat 556650DNAArtificial SequenceProbe SG66
designed to hybridize with cRNA of the human gene ARHGEF2
66ctcaacctct tactgctgtt ctccctttct ccgtccttca tggaagccct
506755DNAArtificial SequenceProbe SG67 designed to hybridize with
cRNA of the human gene C5orfl3 67ccattggcct gagtttcttg tgcattactc
ctctccctcc ttcgttagaa taggt 556852DNAArtificial SequenceProbe SG68
designed to hybridize with cRNA of the human gene XBP1 68gcatcctggc
ttgcctccag ttttaggtcc tttagtttgc ttctgtaagc aa 526950DNAArtificial
SequenceProbe SG69 designed to hybridize with cRNA of the human
gene G1P2 69agcatccgag caggatcaag ggccggaaat aaaggctgtt gtaagagaat
507053DNAArtificial SequenceProbe SG70 designed to hybridize with
cRNA of the human gene GLUD1 70gcccctactc acctgacttt gtatcctctc
cttttagagg ctttgcattc tgc 537155DNAArtificial SequenceProbe SG71
designed to hybridize with cRNA of the human gene S100A2
71ctgccatgga tctcttgggc ccaggactgt tgatgccttt gagttttgta ttcaa
557250DNAArtificial SequenceProbe SG72 designed to hybridize with
cRNA of the human gene LASP1 72tactaagaat aacaagaagc ccagtggtga
ggaaagtgcg ttctcccagc 507350DNAArtificial SequenceProbe SG73
designed to hybridize with cRNA of the human gene TIA-2
73tgtgaaaaat aacagtccac cccaagtcat acactggacc cagtgcctgc
507455DNAArtificial SequenceProbe SG74 designed to hybridize with
cRNA of the human gene PGRMC1 74cctgaaccac gaggaaacag tacagtcgct
agtcaagtgg tttttaaagt aaagt 557550DNAArtificial SequenceProbe SG75
designed to hybridize with cRNA of the human gene ZFPL1
75caagcctaag acactaagac cccagaccca aagccaagtc caccagagtg
507650DNAArtificial SequenceProbe SG76 designed to hybridize with
cRNA of the human gene MAP4K1 76atatggtgat ggtgttgatg gatggctctg
tgaagctggt gaccccggag 507755DNAArtificial SequenceProbe SG77
designed to hybridize with cRNA of the human gene STAT1
77gtggcactgc atacaatctg aggcctcctc tctcagtttt tatatagatg gcgag
557854DNAArtificial SequenceProbe SG78 designed to hybridize with
cRNA of the human gene HNRPH3 78gctgaattct agccctagat tttggagtaa
aaccccttca gcacttgacc gaaa 547953DNAArtificial SequenceProbe SG79
designed to hybridize with cRNA of the human gene TMEM4
79tcaagtttgc gtgtgagagc attgtggagg aatacgagga tgaactcatt gaa
538051DNAArtificial SequenceProbe SG80 designed to hybridize with
cRNA of the human gene KIAA0247 80gtttggtctg aatggtgtag ttgctggttc
cctagagagg aaaaggtggc a 518155DNAArtificial SequenceProbe SG81
designed to hybridize with cRNA of the human gene RIS1 81gtggcctggt
gggcgtttct tcttgtactt atgtggtttt ttggctttta ataca
558253DNAArtificial SequenceProbe SG82 designed to hybridize with
cRNA of the human gene ARS2 82tcttcaacaa gcatgcagag aaaattgagg
aagtgaaaaa ggaagtcgcg ttt 538350DNAArtificial SequenceProbe SG83
designed to hybridize with cRNA of the human gene CA12 83catccactgg
ctgaatgatc agggaggcat agcagtgaga gccataggtc 508455DNAArtificial
SequenceProbe SG84 designed to hybridize with cRNA of the human
gene EEF1B2 84actgcttttg aggactatgt gcagtccatg gatgtggctg
ctttcaacaa gatct 558555DNAArtificial SequenceProbe SG85 designed to
hybridize with cRNA of the human gene TRIB2 85gcctgtatat gttttgtgaa
atggtcctgt ttttgggtag gtgacacgtg gactc 558655DNAArtificial
SequenceProbe SG86 designed to hybridize with cRNA of the human
gene FLJ22169 86agcgtccagc tcccctcaac gctatatttt gacactaaaa
aagaaggttt ctaaa 558750DNAArtificial SequenceProbe SG87 designed to
hybridize with cRNA of the human gene ASNS 87aaagaaggat attactaccg
tcaagtcttt gaacgccatt acccaggccg 508855DNAArtificial SequenceProbe
SG88 designed to hybridize with cRNA of the human gene WBSCR20C
88ggtgagcaaa agtgttgcct gcagaaataa aatgcagaac gtactctacg ataaa
558951DNAArtificial SequenceProbe SG89 designed to hybridize with
cRNA of the human gene AKR1A1 89atcctctgta cccctttaat gacccgtact
gagaccacag cttcttggcc t 519055DNAArtificial SequenceProbe SG90
designed to hybridize with cRNA of the human gene SPRR1A
90cgggtgcatt tgaggatgga tttggggagg gatcaagtga accatcccta gtctt
559150DNAArtificial SequenceProbe SG91 designed to hybridize with
cRNA of the human gene EFNB1 91attaatgtct taattggctg ttgcctgggg
aacaggagag ctgctgcagg 509250DNAArtificial SequenceProbe SG92
designed to hybridize with cRNA of the human gene RPS5 92tcaatgctgc
caagggctcc tcgaactcct atgccattaa gaagaaggac 509351DNAArtificial
SequenceProbe SG93 designed to hybridize with cRNA of the human
gene RPS9 93tgctggattg tctcgttttc ctgccaaata aacaggatca gcgctttaaa
a 519455DNAArtificial SequenceProbe SG94 designed to hybridize with
cRNA of the human gene RPL17 94acggaaaagg aacagattgt tcctaaacca
gaagaggagg ttgcccagaa gaaaa 559555DNAArtificial SequenceProbe SG95
designed to hybridize with cRNA of the human gene ETS2 95cgctgcctca
atacccacaa aagaccattc ccagtataca taagcacagg atgtt
559655DNAArtificial SequenceProbe SG96 designed to hybridize with
cRNA of the human gene EIF4B 96tccttgcctg ctcctgatgc ttggacccct
tttattgatc agagtgctct agaat 559750DNAArtificial SequenceProbe SG97
designed to hybridize with cRNA of the human gene ZYX 97tttgatgtct
agcccctccc atttccaacc cctccctagc atcccaggtg 509855DNAArtificial
SequenceProbe SG98 designed to hybridize with cRNA of the human
gene XPO6 98cggacagtcc tttctccagc ccgacatcca cctttttaaa caaaatctct
tctac 559955DNAArtificial SequenceProbe SG99 designed to hybridize
with cRNA of the human gene LOC285148 99gtcaatacgt agaggtacgc
ttttttcctc aggcttaaac ctttgccact gatat 5510050DNAArtificial
SequenceProbe SG100 designed to hybridize with cRNA of the human
gene C21orf33 100aataaacgcc ttcccaaaat ggcaacttcc cacagccaca
tttcagacct 5010150DNAArtificial SequenceProbe SG101 designed to
hybridize with cRNA of the human gene EEF1D 101agtgtcgata
tcgcagcttt caacaagatc
tgaagcctga gtgtgtgtac 5010251DNAArtificial SequenceProbe SG102
designed to hybridize with cRNA of the human gene PABPC1
102tactacaagc ccaccaagct aaagaggctg cccagaaagc agttaacagt g
5110355DNAArtificial SequenceProbe SG103 designed to hybridize with
cRNA of the human gene RBBP6 103gccagctcag cagaaagtca ggacagcaag
aagaagaaga aaaagaagga aaaga 5510450DNAArtificial SequenceProbe
SG104 designed to hybridize with cRNA of the human gene HRAS
104tttgaggaca tccaccagta cagggagcag atcaaacggg tgaaggactc
5010550DNAArtificial SequenceProbe SG105 designed to hybridize with
cRNA of the human gene GGA3 105tactccaagc ctccgtcaca aaaaaaaaat
caccagctgc catagacacg 5010654DNAArtificial SequenceProbe SG106
designed to hybridize with cRNA of the human gene CFL1
106cctgtatttt ttttaacaac atccccattc cccacctggt cctccccctt ccca
5410755DNAArtificial SequenceProbe SG107 designed to hybridize with
cRNA of the human gene EIF3S2 107gtcattgcac tccatcctga gccacaagag
caaaactccg tctcaaaaaa aaaaa 5510855DNAArtificial SequenceProbe
SG108 designed to hybridize with cRNA of the human gene KRT18
108gcagggtacc ctttggggag caggaggcca ataaaaagtt cagagttcaa aaaaa
5510950DNAArtificial SequenceProbe SG109 designed to hybridize with
cRNA of the human gene IGFIR 109gaaatggaga ataatccagt cctagcacct
ccaagcctga gcaagatgat 5011050DNAArtificial SequenceProbe SG110
designed to hybridize with cRNA of the human gene IL8 110agtgattgag
agtggaccac actgcgccaa cacagaaatt attgtaaagc 5011150DNAArtificial
SequenceProbe SG111 designed to hybridize with cRNA of the human
gene IRF1 111ccggacagca ccagtgatct gtacaacttc caggtgtcac ccatgccctc
5011250DNAArtificial SequenceProbbe SG112 designed to hybridize
with cRNA of the human gene IRF2 112tcatcaagaa aacatcggat
atcacccagg cccgcgtcaa gagctgttaa 5011350DNAArtificial SequenceProbe
SG113 designed to hybridize with cRNA of the human gene LYN
113tatgtgagag atccaacgtc caataaacag caaaggccag ttccagaatc
5011450DNAArtificial SequenceProbe SG114 designed to hybridize with
cRNA of the human gene LYZ 114gttgtcaaaa cagagatgtc cgtcagtatg
ttcaaggttg tggagtgtaa 5011550DNAArtificial SequenceProbe SG115
designed to hybridize with cRNA of the human gene NFKB1A
115gaggacgagc tgccctatga tgactgtgtg tttggaggcc agcgtctgac
5011650DNAArtificial SequenceProbe SG116 designed to hybridize with
cRNA of the human gene MAZ 116ccagccctgg tcttgtcttt tcatccctct
tccccacgac agaagaagtt 5011750DNAArtificial SequenceProbe SG117
designed to hybridize with cRNA of the human gene CD79A
117caccaagaac cgaatcatca cagccgaggg gatcatcctc ctgttctgcg
5011850DNAArtificial SequenceProbe SG118 designed to hybridize with
cRNA of the human gene MCM3 118gaggaaatgc ctcaagtaca cactccaaag
acggcagact cacaggagac 5011950DNAArtificial SequenceProbe SG119
designed to hybridize with cRNA of the human gene MEIS1
119gtttcgtaat ggacggtcag caacatatgg gaattagagc accaggacct
5012050DNAArtificial SequenceProbe SG120 designed to hybridize with
cRNA of the human gene PRTN3 120cttcgtgatc tggggatgtg ccacccgcct
tttccctgac ttcttcacgc 5012150DNAArtificial SequenceProbe SG121
designed to hybridize with cRNA of the human gene MMP2
121gaaccaaagt ctgaagagcg tgaagtttgg aagcatcaaa tccgactggc
5012250DNAArtificial SequenceProbe SG122 designed to hybridize with
cRNA of the human gene MMP7 122gtagcagtct agggattaac ttcctgtatg
ctgcaactca tgaacttggc 5012350DNAArtificial SequenceProbe SG123
designed to hybridize with cRNA of the human gene MMP8
123ttaccagagt tgcaagaggc aataaatggc ttaactgtag atatggctga
5012450DNAArtificial SequenceProbe SG124 designed to hybridize with
cRNA of the human gene DOK1 124cctggtactg caactggcag tggcatcaaa
agccacaact cagccctgta 5012550DNAArtificial SequenceProbe SG125
designed to hybridize with cRNA of the human gene PDGFA
125ccgctgtctg caagaccagg acggtcattt acgagattcc tcggagtcag
5012650DNAArtificial SequenceProbe SG126 designed to hybridize with
cRNA of the human gene PRL 126attatctcaa gctcctgaag tgccgaatca
tccacaacaa caactgctaa 5012750DNAArtificial SequenceProbe SG127
designed to hybridize with cRNA of the human gene RAF1
127ctattggtga tagtggagtc ccagcactac cttctttgac tatgcgtcgt
5012850DNAArtificial SequenceProbe SG128 designed to hybridize with
cRNA of the human gene RARB 128tcagtggatt gacccaaacc gaatggcagc
atcggcacac tgctcaatca 5012950DNAArtificial SequenceProbe SG129
designed to hybridize with cRNA of the human gene OPRD1
129acggtgacca agatctgcgt gttcctcttc gccttcgtgg tgcccatcct
5013050DNAArtificial SequenceProbe SG130 designed to hybridize with
cRNA of the human gene RET 130caggcaggtg tgagtggagg caaggagatg
gcaaagggat caccaggaac 5013150DNAArtificial SequenceProbe SG131
designed to hybridize with cRNA of the human gene SREBF1
131ttggtgcttc tctttgtcta cggtgagcca gtcacacggc cccactcagg
5013250DNAArtificial SequenceProbe SG132 designed to hybridize with
cRNA of the human gene TNF 132agccctctgg cccaggcagt cagatcatct
tctcgaaccc cgagtgacaa 5013350DNAArtificial SequenceProbe SG133
designed to hybridize with cRNA of the human gene TERF1
133cctgggtgac aggatcatac gtaccccaaa cctcaacatc acacagtata
5013450DNAArtificial SequenceProbe SG134 designed to hybridize with
cRNA of the human gene VCAM1 134tctcccctgg accccggatt gctgctcaga
ttggagactc agtcatgttg 5013550DNAArtificial SequenceProbe SG135
designed to hybridize with cRNA of the human gene ATP5O
135ccaagtattg aaattggagg ctaagactga tccgtcaatc ttgggtggaa
5013650DNAArtificial SequenceProbe SG136 designed to hybridize with
cRNA of the human gene TNFSF5 136caggtgcttc ggtgtttgtc aatgtgactg
atccaagcca agtgagccat 5013750DNAArtificial SequenceProbe SG137
designed to hybridize with cRNA of the human gene POLR2C
137gaagaaactg agtgatttac aaactcaatt aagccacgag atccagagtg
5013850DNAArtificial SequenceProbe SG138 designed to hybridize with
cRNA of the human gene PLA2G6 138agctcagccc ccaccgatca gcctaaacaa
cctagaacta caggatctca 5013950DNAArtificial SequenceProbe SG139
designed to hybridize with cRNA of the human gene CCT6A
139tcttggttga tgagatcatg cgagctggaa tgtcttctct gaaaggttga
5014050DNAArtificial SequenceProbe SG140 designed to hybridize with
cRNA of the human gene PDHA1 140ccacagacca tctcatcaca gcctaccggg
ctcacggctt tactttcacc 5014150DNAArtificial SequenceProbe SG141
designed to hybridize with cRNA of the human gene LADH
141cggaataaag gatgatgtct tccttagtgt tccttgcatt ttgggacaga
5014250DNAArtificial SequenceProbe SG142 designed to hybridize with
cRNA of the human gene SNRPB 142gaactccaaa caagcagaaa gggaagagaa
gcgagtcctc ggtctggtgc 5014350DNAArtificial SequenceProbe SG143
designed to hybridize with cRNA of the human gene SNRPB
143tacaaacccg aggaccctct tagggaagaa gccctacatt tgcagtgatt
5014450DNAArtificial SequenceProbe SG144 designed to hybridize with
cRNA of the human gene H2AFX 144aggcgccctc gggcggcaag aaggccaccc
aggcctccca ggagtactaa 5014550DNAArtificial SequenceProbe SG145
designed to hybridize with cRNA of the human gene MRPL37
145ggctatcctt acccctatcc ccataccctg tacttactgg acaaagccaa
5014650DNAArtificial SequenceProbe SG146 designed to hybridize with
cRNA of the human gene UBE2C 146cctgctatca ccccaacgtg gacacccagg
gtaacatatg cctggacatc 5014750DNAArtificial SequenceProbe SG147
designed to hybridize with cRNA of the human gene RPS3
147aagaaagcat tcatgggacc actgaagaaa gaccgaattg caaaggaaga
5014850DNAArtificial SequenceProbe SG148 designed to hybridize with
cRNA of the human gene ALDH1A1 148actgggagag tacggtttcc atgaatatac
agaggtcaaa acagtcacag 5014950DNAArtificial SequenceProbe SG149
designed to hybridize with cRNA of the human gene AF1q
149gcagaccagg agaaaaaccc tgaaggtgat ggcctccttg agtacagcac
5015050DNAArtificial SequenceProbe SG150 designed to hybridize with
cRNA of the human gene RUNX1 150ctccctgaac cactccactg cctttaaccc
tcagcctcag agtcagatgc 5015150DNAArtificial SequenceProbe SG151
designed to hybridize with cRNA of the human gene MYBL1
151atgggaagac agaagaccaa cttattatga ctgaacaagc aagaagatat
5015250DNAArtificial SequenceProbe SG152 designed to hybridize with
cRNA of the human gene ANXA6 152tgagaaatat gacaagtctc tccaccaagc
cattgagggt gacacctccg 5015350DNAArtificial SequenceProbe SG153
designed to hybridize with cRNA of the human gene ALK 153gtcattacga
ggataccatt ctgaaaagca agaatagcat gaaccagcct 5015450DNAArtificial
SequenceProbe SG154 designed to hybridize with cRNA of the human
gene MNDA 154gtgtgagaaa ggagataaac ttcgactctt ctgccttcaa ctgagaacag
5015550DNAArtificial SequenceProbe SG155 designed to hybridize with
cRNA of the human gene APAF1 155ggtggaacgt tgtcactggg gaatcctcac
agaccttcta cacaaatgga 5015650DNAArtificial SequenceProbe SG156
designed to hybridize with cRNA of the human gene BIRC3
156aggcgacact ttcctaattg cttctttgtt ttgggccgga atcttaatat
5015750DNAArtificial SequenceProbe SG157 designed to hybridize with
cRNA of the human gene ABCC6 157tgtccttcaa gatccacgca ggagagaagg
tgggcatcgt tggcaggacc 5015850DNAArtificial SequenceProbe SG158
designed to hybridize with cRNA of the human gene ATIC
158gaactgggaa tcatcctcgc tcatacgaac cttcggctct tccaccactg
5015950DNAArtificial SequenceProbe SG159 designed to hybridize with
cRNA of the human gene ATM 159tgaggaatta gatgaacgtg agcgaaactc
tcgtccttct agtaaaaatc 5016050DNAArtificial SequenceProbe SG160
designed to hybridize with cRNA of the human gene BAX 160ttgtcgccct
tttctacttt gccagcaaac tggtgctcaa ggccctgtgc 5016150DNAArtificial
SequenceProbe SG161 designed to hybridize with cRNA of the human
gene CCND1 161cttcctgtcc tactaccgcc tcacacgctt cctctccaga
gtgatcaagt 5016250DNAArtificial SequenceProbe SG162 designed to
hybridize with cRNA of the human gene BCL2 162ttgctgggac tgtacccaag
aattaaacca agacaaagga gcttggcctg 5016350DNAArtificial SequenceProbe
SG163 designed to hybridize with cRNA of the human gene BCL3
163tttcctctgg tgaacctgcc tacaccccta taccccatga tgtgccccat
5016450DNAArtificial SequenceProbe SG164 designed to hybridize with
cRNA of the human gene BCL6 164tcaataacat cgttaacagg tccatgacgg
gctctccccg cagcagcagc 5016550DNAArtificial SequenceProbe SG165
designed to hybridize with cRNA of the human gene BCL7A
165gttgtcgggg gatctggaag gagtgccacc ctctaaaaag atgaaactgg
5016650DNAArtificial SequenceProbe SG166 designed to hybridize with
cRNA of the human gene BCL7b 166caaggaagaa ccagttccac tagagacaca
ggtcgttgag gaagaggaag 5016750DNAArtificial SequenceProbe SG167
designed to hybridize with cRNA of the human gene BCL10
167gcacgacgcc ctttttttct actaattctt ctctgaattt gcctgttcta
5016850DNAArtificial SequenceProbe SG168 designed to hybridize with
cRNA of the human gene BCL2L1 168gtagacaagg agatgcaggt attggtgagt
cggatcgcag cttggatggc 5016950DNAArtificial SequenceProbe SG169
designed to hybridize with cRNA of the human gene BCR 169gcagggagtt
cagcttgaag aggatgccgt cccgaaaaca gacaggggtc 5017050DNAArtificial
SequenceProbe SG170 designed to hybridize with cRNA of the human
gene BCR 170aatgtctgag gaagcatcgg agactgggtc ccgccatgcc tgtgtcatct
5017150DNAArtificial SequenceProbe SG171 designed to hybridize with
cRNA of the human gene OLIG2 171caactacatc ctcatgctca ccaactcgct
ggaggagatg aagcgactgg 5017250DNAArtificial SequenceProbe SG172
designed to hybridize with cRNA of the human gene BIK 172caccacactt
aaggagaaca taatgaggtt ctggagatcc ccgaaccccg 5017350DNAArtificial
SequenceProbe SG173 designed to hybridize with cRNA of the human
gene BCL2LAA 173cagagccaca aggtaatcct gaaggcaatc acggaggtga
aggggacagc 5017450DNAArtificial SequenceProbe SG174 designed to
hybridize with cRNA of the human gene BMI1 174caatagacct cgaaaatcat
cagtaaatgg gtcatcagca acttcttctg 5017550DNAArtificial SequenceProbe
SG175 designed to hybridize with cRNA of the human gene BLMH
175ctaggcccca gcacaagtac aacaaacttt acacagtgga atacttaagc
5017650DNAArtificial SequenceProbe SG176 designed to hybridize with
cRNA of the human gene BLR1 176ttctgggaac tggacagatt ggacaactat
aacgacacct ccctggtgga 5017750DNAArtificial SequenceProbe SG177
designed to hybridize with cRNA of the human gene IBSP
177cgtcaatgaa tacgacaatg gatatgaaat ctatgaaagt gagaacgggg
5017850DNAArtificial SequenceProbe SG178 designed to hybridize with
cRNA of the human gene BTG1 178gtagcactca aaacagcacc aacgtgcaaa
tggtagacag ccgaatcagc 5017950DNAArtificial SequenceProbe SG179
designed to hybridize with cRNA of the human gene BUB1
179gaaatacaat caacggagaa agcatgagca atgggtaaat gaagacagac
5018050DNAArtificial SequenceProbe SG180 designed to hybridize with
cRNA of the human gene ABL1 180gcaagctcct cagttcggtg aaggaaatca
gtgacatagt gcagaggtag 5018150DNAArtificial SequenceProbe SG171
designed to hybridize with cRNA of the human gene CASP1
181ggactctcag cagatcaaac atctggaaat taccttaata tgcaagactc
5018250DNAArtificial SequenceProbe SG182 designed to hybridize with
cRNA of the human gene CASP3 182cctggttatt attcttggcg aaattcaaag
gatggctcct ggttcatcca 5018350DNAArtificial SequenceProbe SG183
designed to hybridize with cRNA of the human gene CASP4
183aaatatcccc caataaaaaa gctcatccga atatggaggc tggaccacct
5018450DNAArtificial SequenceProbe SG184 designed to hybridize with
cRNA of the human gene CASP5 184ctggacaaac atctatccag accctagtac
ctaatacgga tcaaaagtcg 5018550DNAArtificial SequenceProbe SG185
designed to hybridize with cRNA of the human gene CASP6
185ggttccctgt tttgcctcaa tgctaactaa aaagctgcat ttctttccaa
5018650DNAArtificial SequenceProbe SG186 designed to hybridize with
cRNA of the human gene CASP7 186tcccctgtgt ggtctccatg ctcaccaagg
aactctactt cagtcaatag 5018750DNAArtificial SequenceProbe SG187
designed to hybridize with cRNA of the human gene CASP8
187gcagcagcct tgaaggaagt cctgatgaat tttcaaatga ctttggacaa
5018850DNAArtificial SequenceProbe SG188 designed to hybridize with
cRNA of the human gene CASP9 188gtccctcctg cttagggtcg ctaatgctgt
ttcggtgaaa gggatttata 5018950DNAArtificial SequenceProbe SG189
designed to hybridize with cRNA of the human gene CBFB
189gctcccatga ttctgaatgg agtctgtgtt atctggaaag gctggattga
5019050DNAArtificial SequenceProbe S90 designed to hybridize with
cRNA of the human gene CALD1 190caaaagaggg aggagatgcg actcgaagca
gaaagaatcg cctaccagag 5019150DNAArtificial SequenceProbe SG191
designed to hybridize with cRNA of the human gene CAST
191agcaggcatc agatacagga agtaacgatg ctcacaataa aaaagcagtt
5019250DNAArtificial SequenceProbe SG192 designed to hybridize with
cRNA of the human gene CDC25A 192caggggagaa gagcaagagg gagatgtaca
gtcgtctgaa gaagctctga 5019350DNAArtificial SequenceProbe SG193
designed to hybridize with cRNA of the human gene CDC25B
193ttccctcagc acccgaactt ctgtgaaccc caggactacc ggcccatgaa
5019450DNAArtificial SequenceProbe SG194 designed to hybridize with
cRNA of the human gene CD2 194aaattccagc ttcaacccct cagaatccag
caacttccca acatcctcct 5019550DNAArtificial SequenceProbe SG195
designed to hybridize with cRNA of the human gene CD3E
195aagatgcgaa cttttatctc tacctgaggg caagagtgtg tgagaactgc
5019650DNAArtificial SequenceProbe SG196 designed to hybridize with
cRNA of the human gene CD4 196ctccaaccag ataaagattc tgggaaatca
gggctccttc ttaactaaag 5019750DNAArtificial SequenceProbe SG197
designed to hybridize with cRNA of the human gene CD5 197ggaaaatatg
ccctccccgt aatggtgaac caccagcacc tacccaccac 5019850DNAArtificial
SequenceProbe SG198 designed to hybridize with cRNA of the human
gene CD6 198tcatctaaag acaccttcct ttccactggc tgtcaagcca cagggcacca
5019950DNAArtificial SequenceProbe SG199 designed to hybridize with
cRNA of the human gene CD7 199gtgctcgtgg cgggataaga attcggcggc
atgtgtggtg tacgaggaca 5020050DNAArtificial SequenceProbe SG200
designed to hybridize with cRNA of the human gene CD8 200ttcattctca
atctcacaag cgtgaagccg gaagacagtg gcatctactt 5020150DNAArtificial
SequenceProbe SG201 designed to hybridize with cRNA of the human
gene CD9 201gtgaagtcct gtcctgatgc catcaaagag gtcttcgaca ataaattcca
5020250DNAArtificial SequenceProbe SG202
designed to hybridize with cRNA of the human gene MME 202tcagaagcct
ttcactgccg caagaattca tacatgaatc cagaaaagaa 5020350DNAArtificial
SequenceProbe SG203 designed to hybridize with cRNA of the human
gene ITGAL 203tgcctgaagc ccctccatga gaaggactct gagagtggtg
gtggcaagga 5020450DNAArtificial SequenceProbe SG204 Designed to
hybridize with cRNA of the human gene ITGAM 204tttgtgaggt
cccagacgga gaccaaagtg gagccgttcg aggtccccaa 5020550DNAArtificial
SequenceProbe SG205 Designed to hybridize with cRNA of the human
gene ITGAX 205aggaggcaaa tggacaaatt gccccagaaa acgggacaca
gacccccagc 5020650DNAArtificial SequenceProbe SG206 Designed to
hybridize with cRNA of the human gene ANPEP 206agccctggag
aagacgaaag ccaacatcaa gtgggtgaag gagaacaagg 5020750DNAArtificial
SequenceProbe SG207 Designed to hybridize with cRNA of the human
gene CD14 207tggataacct gacactggac gggaatccct tcctggtccc tggaactgcc
5020850DNAArtificial SequenceProbe SG208 Designed to hybridize with
cRNA of the human gene SELE 208aattgggctc ctgcacacag tggcccgcta
caagttctac ctggctttcg 5020950DNAArtificial SequenceProbe SG209
Designed to hybridize with cRNA of the human gene FCGR3A
209gtgaagacaa acattcgaag ctcaacaaga gactggaagg accataaatt
5021050DNAArtificial SequenceProbe SG210 Designed to hybridize with
cRNA of the human gene FCGR3B 210gcttggtgat ggtactcctt tttgcagtgg
acacaggact atatttctct 5021150DNAArtificial SequenceProbe SG211
Designed to hybridize with cRNA of the human gene ITGB2
211gataatcccc ttttcaagag cgccaccacg acggtcatga accccaagtt
5021250DNAArtificial SequenceProbe SG212 Designed to hybridize with
cRNA of the human gene CD19 212actccattcg gggccagcct ggacccaatc
atgaggaaga tgcagactct 5021350DNAArtificial SequenceProbe SG213
Designed to hybridize with cRNA of the human gene MS4A1
213ctccccaaga tcaggaatcc tcaccaatag aaaatgacag ctctccttaa
5021450DNAArtificial SequenceProbe SG214 Designed to hybridize with
cRNA of the human gene CR2 214catttagaag cacgagaagt atattctgtt
gatccataca acccagccag 5021550DNAArtificial SequenceProbe SG215
Designed to hybridize with cRNA of the human gene CD22
215acgtcattcc agattttcca gaagatgagg ggattcatta ctcagagctg
5021650DNAArtificial SequenceProbe SG216 Designed to hybridize with
cRNA of the human gene FCER2 216actccgggag gaggtgacaa agctaaggat
ggagttgcag gtgtccagcg 5021750DNAArtificial SequenceProbe SG217
Designed to hybridize with cRNA of the human gene CD24
217cagccagtct cttcgtggtc tcactctctc ttctgcatct ctactcttaa
5021850DNAArtificial SequenceProbe SG218 Designed to hybridize with
cRNA of the human gene IL2RA 218ctgctgagag cgtctgcaaa atgacccacg
ggaagacaag gtggacccag 5021950DNAArtificial SequenceProbe SG219
Designed to hybridize with cRNA of the human gene DPP4
219gacaaccttg accattacag aaattcaaca gtcatgagca gagctgaaaa
5022050DNAArtificial SequenceProbe SG220 Designed to hybridize with
cRNA of the human gene ITGB1 220gagaaaatga atgccaaatg ggacacgcaa
gaaaatccga tttacaagag 5022150DNAArtificial SequenceProbe SG221
Designed to hybridize with cRNA of the human gene TNFRSF8
221agacggtcac caagccccag gatatggctg agaaggacac cacctttgag
5022250DNAArtificial SequenceProbe SG222 Designed to hybridize with
cRNA of the human gene CD33 222ttacatggcc ccactgaaac ctcaagctgt
tcaggtgccg cccctactgt 5022350DNAArtificial SequenceProbe SG223
Designed to hybridize with cRNA of the human gene CD34
223cctgctggct gtcttgggca tcactggcta tttcctgatg aatcgccgca
5022450DNAArtificial SequenceProbe SG224 Designed to hybridize with
cRNA of the human gene CD36 224ggcctttgcc tctccagttg aaaacccaga
caactattgt ttctgcacag 5022550DNAArtificial SequenceProbe SG225
Designed to hybridize with cRNA of the human gene CD38
225agtgtggaag tccataattt gcaaccagag aaggttcaga cactagaggc
5022650DNAArtificial SequenceProbe SG226 Designed to hybridize with
cRNA of the human gene TNFRSF5 226acccaggagg atggcaaaga gagtcgcatc
tcagtgcagg agagacagtg 5022750DNAArtificial SequenceProbe SG227
Designed to hybridize with cRNA of the human gene SPN 227acccaggagg
atggcaaaga gagtcgcatc tcagtgcagg agagacagtg 5022850DNAArtificial
SequenceProbe SG228 Designed to hybridize with cRNA of the human
gene CD44 228gagctgtgga ggacagaaag ccaagtggac tcaacggaga ggccagcaag
5022950DNAArtificial SequenceProbe SG229 Designed to hybridize with
cRNA of the human gene CD44v6 229ctgggattgg ttttcatggt tgtttctacc
atcagagtca aagaatcatc 5023050DNAArtificial SequenceProbe SG230
Designed to hybridize with cRNA of the human gene PTPRCCD
230aacattctgt caatggtcct gcaagtccag ccttaaatca aggttcatag
5023150DNAArtificial SequenceProbe SG231 Designed to hybridize with
cRNA of the human gene CD47 231tcaggtgata gcctatatcc tcgctgtggt
tggactgagt ctctgtattg 5023250DNAArtificial SequenceProbe SG232
Designed to hybridize with cRNA of the human gene ITGA2
232agccgaagta ccaacaggag ttataatagg aagtataatt gctggaatcc
5023350DNAArtificial SequenceProbe SG233 Designed to hybridize with
cRNA of the human gene ITGA3 233ctaagaggca gaaggcggag atgaagagcc
agccgtcaga gacagagagg 5023450DNAArtificial SequenceProbe SG234
Designed to hybridize with cRNA of the human gene ITGA4
234cttggactta ttgtacttct gttgatctca tatgttatgt ggaaggctgg
5023550DNAArtificial SequenceProbe SG235 Designed to hybridize with
cRNA of the human gene ITGA5 235tcaactgcac caccaatcac cccattaacc
caaagggcct ggagttggat 5023650DNAArtificial SequenceProbe SG236
Designed to hybridize with cRNA of the human gene ICAM3
236ctatgcagcc gacagaagca atgggggaag aaccgtccag agctgagtga
5023750DNAArtificial SequenceProbe SG237 Designed to hybridize with
cRNA of the human gene CDW52 237ccctcagcat ccagcagcat gagcggaggc
attttccttt tcttcgtggc 5023850DNAArtificial SequenceProbe SG238
Designed to hybridize with cRNA of the human gene ICAM1
238gaacaaccgg aaggtgtatg aactgagcaa tgtgcaagaa gatagccaac
5023950DNAArtificial SequenceProbe SG239 Designed to hybridize with
cRNA of the human gene NCAM1 239gaggtgaccc cagactctga gaatgatttt
gggaactaca actgtactgc 5024050DNAArtificial SequenceProbe SG240
Designed to hybridize with cRNA of the human gene CD58
240catcaatcat tttgacaacc tgtatcccaa gcagcggtca ttcaagacac
5024150DNAArtificial SequenceProbe SG241 Designed to hybridize with
cRNA of the human gene CD59 241cgaacagctt gaaaatggtg ggacatcctt
atcagagaaa acagttcttc 5024250DNAArtificial SequenceProbe SG242
Designed to hybridize with cRNA of the human gene SELL
242taggaacata tggagttttt acaaacgctg catttgaccc gagtccttaa
5024350DNAArtificial SequenceProbe SG243 Designed to hybridize with
cRNA of the human gene CD79B 243gccacctatg aggacatagt gacgctgcgg
acaggggaag tgaagtggtc 5024450DNAArtificial SequenceProbe SG244
Designed to hybridize with cRNA of the human gene CD81
244cttcaaggag gactgccacc agaagatcga tgacctcttc tccgggaagc
5024550DNAArtificial SequenceProbe SG245 Designed to hybridize with
cRNA of the human gene KAI1 245cctgaggtca cctacccctg ttcctgcgaa
gtcaaggggg aagaggacaa 5024650DNAArtificial SequenceProbe SG246
Designed to hybridize with cRNA of the human gene CD83
246caaataagca tttagggcta gtgactcctc acaagacaga actggtatga
5024750DNAArtificial SequenceProbe SG247 Designed to hybridize with
cRNA of the human gene CD86 247caactcttat aaatgtggaa ccaacacaat
ggagagggaa gagagtgaac 5024850DNAArtificial SequenceProbe SG248
Designed to hybridize with cRNA of the human gene TNFRSF6
248cttccaaatg cagaagatgt agattgtgtg atgaaggaca tgatgtgaac
5024950DNAArtificial SequenceProbe SG249 Designed to hybridize with
cRNA of the human gene TNFSF6 249tgaggaactc taagtatccc caggatctgg
tgatgatgga ggggaagatg 5025050DNAArtificial SequenceProbe SG250
Designed to hybridize with cRNA of the human gene SLC7A5
250tgacatccca ggggctgtaa gtgccaacat gactgtgaag ggccagagtg
5025150DNAArtificial SequenceProbe SG251 Designed to hybridize with
cRNA of the human gene SDC1 251aaacaagcca acggcggggc ctaccagaag
cccaccaaac aggaggaatt 5025250DNAArtificial SequenceProbe SG252
Designed to hybridize with cRNA of the human gene CDK4
252ctggaaatgc tgacttttaa cccacacaag cgaatctctg cctttcgagc
5025350DNAArtificial SequenceProbe SG253 Designed to hybridize with
cRNA of the human gene STAT3 253agggcagttt gagtccctca cctttgacat
ggagttgacc tcggagtgcg 5025450DNAArtificial SequenceProbe SG254
Designed to hybridize with cRNA of the human gene FGR 254gactatgagg
ctcgaactga ggatgacctc accttcacca agggcgagaa 5025550DNAArtificial
SequenceProbe SG255 Designed to hybridize with cRNA of the human
gene FOS 255gagcgcagag cattggcagg aggggcaagg tggaacagtt atctccagaa
5025650DNAArtificial SequenceProbe SG256 Designed to hybridize with
cRNA of the human gene CCNE1 256tgtaccaagt ggagcaggtg gttgcgggca
agcgttgtgc agagcccata 5025750DNAArtificial SequenceProbe SG257
Designed to hybridize with cRNA of the human gene CDA 257ccgctatcca
gaaggccgtc tcagaagggt acaaggattt cagggcaatt 5025850DNAArtificial
SequenceProbe SG258 Designed to hybridize with cRNA of the human
gene MAFB 258gcaaggagga ggtgatccgg ctgaagcaga agaggcggac cctgaaaaac
5025950DNAArtificial SequenceProbe SG259 Designed to hybridize with
cRNA of the human gene MPL 259tgctgtacca cccacattgc caaccattcc
tacctaccac taagctattg 5026050DNAArtificial SequenceProbe SG260
Designed to hybridize with cRNA of the human gene MYC 260gttgcggaaa
cgacgagaac agttgaaaca caaacttgaa cagctacgga 5026150DNAArtificial
SequenceProbe SG261 Designed to hybridize with cRNA of the human
gene MYB 261agctaaaagg acagcaggtg ctaccagtaa gactgtcatc atgtgcttga
5026250DNAArtificial SequenceProbe SG262 Designed to hybridize with
cRNA of the human gene CKMT1 262gctggtgcag atggtggtgg acggagtgaa
gctgctcatc gagatggaac 5026350DNAArtificial SequenceProbe SG263
Designed to hybridize with cRNA of the human gene CREBBP
263cacgtctcac cccagactgg ttccccccac cccggactcg cagtcaccat
5026450DNAArtificial SequenceProbe SG264 Designed to hybridize with
cRNA of the human gene CTGF 264catcaagacc tgtgcctgcc attacaactg
tcccggagac aatgacatct 5026550DNAArtificial SequenceProbe SG265
Designed to hybridize with cRNA of the human gene CXCR3
265agctttgacc gctacctgaa catagttcat gccacccagc tctaccgccg
5026650DNAArtificial SequenceProbe SG266 Designed to hybridize with
cRNA of the human gene CXCR4 266attcatctgt ttccactgag tctgagtctt
caagttttca ctccagctaa 5026750DNAArtificial SequenceProbe SG267
Designed to hybridize with cRNA of the human gene CCNA1
267gcaatcatgt accctggatc ttttattggg ggctggggag aagagtatct
5026850DNAArtificial SequenceProbe SG268 Designed to hybridize with
cRNA of the human gene CCNB1 268ggacttacaa agcacatgac tgtcaagaac
aagtatgcca catcgaagca 5026950DNAArtificial SequenceProbe SG269
Designed to hybridize with cRNA of the human gene CCMD2
269aactggacca agccagcacc cctacagacg tgcgggatat cgacctgtga
5027050DNAArtificial SequenceProbe SG270 Designed to hybridize with
cRNA of the human gene CYP1A1 270accaagaact gcttagccta gtcaacctga
ataataattt cggggaggtg 5027150DNAArtificial SequenceProbe SG271
Designed to hybridize with cRNA of the human gene CYP2A6
271gcgcatgatg ctaggaatct tccagttcac gtcaacctcc acggggcagc
5027250DNAArtificial SequenceProbe SG272 Designed to hybridize with
cRNA of the human gene DAD- 272cggtttgcct gagaatacag atcaacccac
agaacaaagc ggatttccaa 5027350DNAArtificial SequenceProbe SG273
Designed to hybridize with cRNA of the human gene TNFRSF10C
273tcatgcacca tcgtagggat catagttcta attgtgcttc tgattgtgtt
5027450DNAArtificial SequenceProbe SG274 Designed to hybridize with
cRNA of the human gene DEK 274acagaaagct acttctaaaa gtaaaaaatc
tgtgaaaagt gccaatgtta 5027550DNAArtificial SequenceProbe SG275
Designed to hybridize with cRNA of the human gene DCK 275gctggctcct
gcataggaca ctgaaaacca acttcgatta tcttcaagag 5027650DNAArtificial
SequenceProbe SG276 Designed to hybridize with cRNA of the human
gene DHFR 276ccaggtgttc tctctgatgt ccaggaggag aaaggcatta agtacaaatt
5027750DNAArtificial SequenceDesigned to hybridize with cRNA of the
human gene TCF3 277tcaggtgtgg ttggagaccc ccagatggtg ctttcagctc
cccacccagg 5027850DNAArtificial SequenceProbe SG278 Designed to
hybridize with cRNA of the human gene E2F1 278tcagagacct cttcgactgt
gactttgggg acctcacccc cctggatttc 5027950DNAArtificial SequenceProbe
SG279 Designed to hybridize with cRNA of the human gene TCF3
279tgccagatgc acctcaagtc ggacaaagcg cagaccaagc tgctcatcct
5028050DNAArtificial SequenceProbe SG280 Designed to hybridize with
cRNA of the human gene EB-1 280tactttgatg atattccccg atcaaaactg
gagaggcaga tggctcagac 5028150DNAArtificial SequenceProbe SG281
Designed to hybridize with cRNA of the human gene CCR7
281gccttcatcg gcgtcaagtt ccgcaacgat ctcttcaagc tcttcaagga
5028250DNAArtificial SequenceProbe SG282 Designed to hybridize with
cRNA of the human gene EBI2 282gtcagtgtat cgatttctag tgctgtgaag
tcagcccctg aagaaaattc 5028350DNAArtificial SequenceProbe SG283
Designed to hybridize with cRNA of the human gene MUC-1
283tacctcctct cacctcctcc aatcacagca cttctcccca gttgtctact
5028450DNAArtificial SequenceProbe SG284 Designed to hybridize with
cRNA of the human gene EphA3 284atgtgggcat tcagctccga cggcccttgt
tccagaaggt aaccacggtg 5028550DNAArtificial SequenceProbe SG285
Designed to hybridize with cRNA of the human gene EPOR
285tcagaagcat cctcctgctc atctgctttg gctaccttcc agcataacta
5028650DNAArtificial SequenceProbe SG286 Designed to hybridize with
cRNA of the human gene ERCC1 286aaacggacag tcagaccctc ctgaccacat
ttggatctct ggaacagctc 5028750DNAArtificial SequenceProbe SG287
Designed to hybridize with cRNA of the human gene ERCC2
287tcaggggcaa gacggactac ggcctcatgg tctttgccga caagcggttt
5028850DNAArtificial SequenceProbe SG288 Designed to hybridize with
cRNA of the human gene ERCC3 288cggcgctttg gcaccatgag ttctatgtct
ggggccgacg acactgtgta 5028950DNAArtificial SequenceProbe SG289
Designed to hybridize with cRNA of the human gene ERCC5
289tagtgatgac gatggaggga aagagaagat ggtcctcgtg accgccagat
5029050DNAArtificial SequenceProbe SG290 Designed to hybridize with
cRNA of the human gene ERCC6 290tgcactttcc atagaacttc tggtggtgaa
ggaatttgga aactcaagcc 5029150DNAArtificial SequenceProbe SG291
Designed to hybridize with cRNA of the human gene CUZD1
291cacagtgagg cattttgtaa atcaacgggc agactacaaa taccagaagc
5029250DNAArtificial SequenceProbe SG292 Designed to hybridize with
cRNA of the human gene ETV6 292aatcatgagt ggccgaacag accgtctgga
gcacctagag tcccaggagc 5029350DNAArtificial SequenceProbe SG293
Designed to hybridize with cRNA of the human gene EIF4E
293attatggaat acaaaactca caccgacagc atcaaaatgc caggcaggct
5029450DNAArtificial SequenceProbe SG294 Designed to hybridize with
cRNA of the human gene EIF5A 294ccttggcaag gagattgagc agaagtacga
ctgtggagaa gagatcctga 5029550DNAArtificial SequenceProbe SG295
Designed to hybridize with cRNA of the human gene EZH2
295tccacggcag ccttgtgaca gttcgtgccc ttgtgtgata gcacaaaatt
5029650DNAArtificial SequenceProbe SG296 Designed to hybridize with
cRNA of the human gene FADD 296atgtccccga tgtcatggaa ctcagacgca
tctacctccg aagcgtcctg 5029750DNAArtificial SequenceProbe SG297
Designed to hybridize with cRNA of the human gene PTK2
297gcacccaccg agagattgag atggcacaga agctattgaa ctctgacctg
5029850DNAArtificial SequenceProbe SG298 Designed to hybridize with
cRNA of the human gene FAT 298ttgtagagaa ccccatgccc cttacccgcc
agggtatcaa agacacttcg 5029950DNAArtificial SequenceProbe SG299
Designed to hybridize with cRNA of the human gene FGFR1
299ttcttctggt tcggccatca cggctctcct ccagtgggac tcccatgcta
5030050DNAArtificial SequenceProbe SG300 Designed to hybridize with
cRNA of the human gene FGFR3 300aggagctaga ggttctctcc ttgcacaacg
tcacctttga ggacgccggg 5030150DNAArtificial SequenceProbe SG301
Designed to hybridize with cRNA of the human gene FHIT
301tcctgcctct tggagatcag aggaggaaat ggcagcagaa gccgcagctc
5030250DNAArtificial SequenceProbe SG302 Designed to hybridize with
cRNA of the human gene FLT3 302tggagcgcgt gaacacggag atacactttg
tcaccaaatg tgcctttcag 5030350DNAArtificial SequenceProbe SG303
Designed to hybridize with cRNA of the human gene GRIA3
303gcgatacttg attgactgcg aagtcgaaag gattaacaca attttggaac
5030450DNAArtificial SequenceProbe SG304 Designed to hybridize with
cRNA of the human gene FUS 304gggacagccc atgattaatt tgtacacaga
cagggaaact ggcaagctga 5030550DNAArtificial SequenceProbe SG305
Designed to hybridize with cRNA of the human gene EIF4E
305cccacgcaga cacagctact aagagcggct ccaccactaa aaataggttt
5030650DNAArtificial SequenceProbe SG306 Designed to hybridize with
cRNA of the human gene SIAT4A 306agactttgag tctaacgtga cggccacctt
ggcctccatc aataaaatcc 5030750DNAArtificial SequenceProbe SG307
Designed to hybridize with cRNA of the human gene CSF3
307gcttcctgga ggtgtcgtac cgcgttctac gccaccttgc ccagccctga
5030850DNAArtificial SequenceProbe SG308 Designed to hybridize with
cRNA of the human gene CSF2 308ccctccaacc ccggaaactt cctgtgcaac
ccagattatc acctttgaaa 5030950DNAArtificial SequenceProbe SG309
Designed to hybridize with cRNA of the human gene NR3C1
309cagccagaac tggcagcggt tttatcaact gacaaaactc ttggattcta
5031050DNAArtificial SequenceProbe SG310 Designed to hybridize with
cRNA of the human gene GSTT1 310ataaggtgat gttccctgtg ttcctgggtg
ggccagtatc tccccagaca 5031150DNAArtificial SequenceProbe SG311
Designed to hybridize with cRNA of the human gene GZMA
311ggcctggtgt ctatattctt ctctcaaaga aacacctcaa ctggataatt
5031250DNAArtificial SequenceProbe SG312 Designed to hybridize with
cRNA of the human gene DNAJA1 312agatcttctg ccatctagac cggaagttcc
taacataatt ggagaaacag 5031350DNAArtificial SequenceProbe SG313
Designed to hybridize with cRNA of the human gene HLF 313gatcctgaca
ccatccaggt cccagtgggt tatgagccag acccagcaga 5031450DNAArtificial
SequenceProbe SG314 Designed to hybridize with cRNA of the human
gene BST2 314agaagagaaa accaggtctt aagcgtgaga atcgcggaca agaagtacta
5031550DNAArtificial SequenceProbe SG315 Designed to hybridize with
cRNA of the human gene HOXA9 315ggggtgactg tcccacgctt gacactcaca
ctttgtccct gactgactat 5031650DNAArtificial SequenceProbe SG316
Designed to hybridize with cRNA of the human gene TLX1
316gacaggttca caggtcaccc ctatcagaac cggacgcccc ccaagaagaa
5031750DNAArtificial SequenceProbe SG317 Designed to hybridize with
cRNA of the human gene UHRF1 317cgctacgatg gcatctacaa ggttgtgaaa
tactggcccg agaaggggaa 5031850DNAArtificial SequenceProbe SG318
Designed to hybridize with cRNA of the human gene IER3
318aaaaggcttc tctttctgct gctcaccatc gtcttctgcc agatcctgat
5031950DNAArtificial SequenceProbe SG319 Designed to hybridize with
cRNA of the human gene IL1B 319cagaccttcc aggagaatga cctgagcacc
ttctttccct tcatctttga 5032050DNAArtificial SequenceProbe SG320
Designed to hybridize with cRNA of the human gene IL2 320agcaaccatt
gtagaatttc tgaacagatg gattaccttt tgtcaaagca 5032150DNAArtificial
SequenceProbe SG321 Designed to hybridize with cRNA of the human
gene IL3 321gcacccacgc gacatccaat ccatatcaag gacggtgact ggaatgaatt
5032250DNAArtificial SequenceProbe SG322 Designed to hybridize with
cRNA of the human gene IL6 322gaacaagcca gagctgtcca gatgagtaca
aaagtcctga tccagttcct 5032350DNAArtificial SequenceProbe SG323
Designed to hybridize with cRNA of the human gene IL6R
323cacggagccc ttatgacatc agcaatacag actacttctt ccccagatag
5032450DNAArtificial SequenceProbe SG324 Designed to hybridize with
cRNA of the human gene IL10 324ccaagagaaa ggcatctaca aagccatgag
tgagtttgac atcttcatca 5032550DNAArtificial SequenceProbe SG325
Designed to hybridize with cRNA of the human gene IL15
325atacggaaag tgatgttcac cccagttgca aagtaacagc aatgaagtgc
5032650DNAArtificial SequenceProbe SG326 Designed to hybridize with
cRNA of the human gene IRF4 326atccagaaga ttaccacaga tctatccgcc
attcctctat tcaagaatga 5032750DNAArtificial SequenceProbe SG327
Designed to hybridize with cRNA of the human gene JAK1
327aacgcctgcc gtgcccacct aactgtccag atgaggttta tcagcttatg
5032850DNAArtificial SequenceProbe SG328 Designed to hybridize with
cRNA of the human gene JAK2 328aatcaacgcc cctcctttag ggatctagct
cttcgagtgg atcaaataag 5032950DNAArtificial SequenceProbe SG329
Designed to hybridize with cRNA of the human gene MKI67
329tgtgtcaaga aaataacaac cagaagtcat agggacagtg aagatatttg
5033050DNAArtificial SequenceProbe SG330 Designed to hybridize with
cRNA of the human gene XRCC5 330tgggaaattg ttgtccagga tggaattact
ctgatcacca aagaggaagc 5033150DNAArtificial SequenceProbe SG331
Designed to hybridize with cRNA of the human gene LAG3
331agcaagggat tcaccctcgc caggctcaga cgcaagatag aggagctgga
5033250DNAArtificial SequenceProbe SG332 Designed to hybridize with
cRNA of the human gene LCK 332cccttcaggc atcaagttga ccatcaacaa
actcctggac atggcagccc 5033350DNAArtificial SequenceProbe SG333
Designed to hybridize with cRNA of the human gene LCP1
333tttcaaggac ccgaagatta gtacaagtct gcctgttctg gacctcatcg
5033450DNAArtificial SequenceProbe SG334 Designed to hybridize with
cRNA of the human gene LEPR 334agaattgttc ctgggcacaa ggacttaatt
ttcagaagag aacggacatt 5033550DNAArtificial SequenceProbe SG335
Designed to hybridize with cRNA of the human gene LMO2
335tgtgcgaaca ggacatctac gagtggacta agatcaatgg gatgatatag
5033650DNAArtificial SequenceProbe SG336 Designed to hybridize with
cRNA of the human gene LIF 336cgtgacggac ttcccgccct tccacgccaa
cggcacggag aaggccaagc 5033750DNAArtificial SequenceProbe SG337
Designed to hybridize with cRNA of the human gene LRP 337ctggaccagt
cagaagccga gaaagctcgc aaggaacttt tggagctgga 5033850DNAArtificial
SequenceProbe SG338 Designed to hybridize with cRNA of the human
gene LSP1 338ggaccgagtc cctaaaccgc tccatagaga agagtaacag tgtgaagaaa
5033950DNAArtificial SequenceProbe SG339 Designed to hybridize with
cRNA of the human gene LYL1 339agtgtctaca ttgggccagc aggacctttt
agcatcttcc ctagcagccg 5034050DNAArtificial SequenceProbe SG340
Designed to hybridize with cRNA of the human gene NFKB1
340catccttccg caaactcagc tttaccgagt ctctgaccag tggtgcctca
5034150DNAArtificial SequenceProbe SG341 Designed to hybridize with
cRNA of the human gene MAL 341caccttgatc atcctgtaca taattggagc
ccacggtgga gagacttcct 5034250DNAArtificial SequenceProbe SG342
Designed to hybridize with cRNA of the human gene MAGEA1
342ctcctcccct cctctcctct cagctagtcc atgtttctcc aacacaagtt
5034350DNAArtificial SequenceProbe SG343 Designed to hybridize with
cRNA of the human gene MAPK10 343agactaaaaa tggtgtagta aaaggacagc
cttctccttc agcacaggtg 5034450DNAArtificial SequenceProbe SG344
Designed to hybridize with cRNA of the human gene MBP1
344ccatgcagag tctgtcctcc cagtcggtgc agcaaactca gggaagccat
5034550DNAArtificial SequenceProbe SG345 Designed to hybridize with
cRNA of the human gene MCL1 345ggctcccagt gactactttt tgacttctgt
ttgtcttacg cttctctcag 5034650DNAArtificial SequenceProbe SG346
Designed to hybridize with cRNA of the human gene MDM2
346tgaatctctc gactcagaag attatagcct tagtgaagaa ggacaagaac
5034750DNAArtificial SequenceProbe SG347 Designed to hybridize with
cRNA of the human gene ABCB1 347tagctcgtgc ccttgttaga cagcctcata
ttttgctttt ggatgaagcc 5034850DNAArtificial SequenceProbe SG348
Designed to hybridize with cRNA of the human gene ABCB4
348tagcgatttt tggaccaggc gatgatgcag tgaagcagca gaagtgcaac
5034950DNAArtificial SequenceProbe SG349 Designed to hybridize with
cRNA of the human gene MEN1 349attgcctcag ccaagaccta ctatcgggat
gaacacatct acccctacat 5035050DNAArtificial SequenceProbe SG350
Designed to hybridize with cRNA of the human gene CXCL9
350gaaggaactg attaaaaagt gggagaaaca ggtcagccaa aagaaaaagc
5035150DNAArtificial SequenceProbe SG351 Designed to hybridize with
cRNA of the human gene MLF1 351ggggacaaac tccacatcaa aggctcatct
gtgaaaagca acaaaaaata 5035250DNAArtificial SequenceProbe SG352
Designed to hybridize with cRNA of the human gene MLL 352gaaaacagga
ccattgccca tagtccaaca tcttttacag aaagttcatc 5035350DNAArtificial
SequenceProbe SG353 Designed to hybridize with cRNA of the human
gene MMP9 353agtgagttga accaggtgga ccaagtgggc tacgtgacct atgacatcct
5035450DNAArtificial SequenceProbe SG354 Designed to hybridize with
cRNA of the human gene NDUFB 354ccggaacaag agtatgttat ttaaaaggga
attgcaaccc agtgaagaag 5035550DNAArtificial SequenceProbe SG355
Designed to hybridize with cRNA of the human gene MPO 355atcaccaccg
tgtctaagaa caacatcttc atgtccaact catatccccg 5035650DNAArtificial
SequenceProbe SG356 Designed to hybridize with cRNA of the human
gene ABCC3 356ccaggtaaag caaatgaaat tgaaggactc gcgcatcaag
ctgatgagtg 5035750DNAArtificial SequenceProbe SG357 Designed to
hybridize with cRNA of the human gene ABCC5 357catcggtcct
tctgtccaac gacagttccc gattctatgc catgtttgct 5035850DNAArtificial
SequenceProbe SG358 Designed to hybridize with cRNA of the human
gene MTCP1 358cagatacagc atcatttaat ggtcagggga gtacaggagc
tgttgcttaa 5035950DNAArtificial SequenceProbe SG359 Designed to
hybridize with cRNA of the human gene MTCP1 359gtgttgtgct
cagtatccca agggaagatc tgtcgtctgt tcaggatttg 5036050DNAArtificial
SequenceProbe SG360 Designed to hybridize with cRNA of the human
gene MYOD1 360ttgccacaac ggacgacttc tatgacgacc cgtgtttcga
ctccccggac 5036150DNAArtificial SequenceProbe SG361 Designed to
hybridize with cRNA of the human gene MX1 361cgtcctgtcg gagccctgtc
tctctctctg taataaactc atttctagca 5036250DNAArtificial SequenceProbe
SG362 Designed to hybridize with cRNA of the human gene NINJ1
362agtacgacct taacaacccg gacaagcacg ccaagctgga cttcctcaac
5036350DNAArtificial SequenceProbe SG363 Designed to hybridize with
cRNA of the human gene NPM1 363tagagtgatg gattgatacc tagcagcctg
tgaaaaggaa tcagtgaatt 5036450DNAArtificial SequenceProbe SG364
Designed to hybridize with cRNA of the human gene IL32
364aggaggagct gacaccccag aagtgctctg aaccccaatc ctcaaaatga
5036550DNAArtificial SequenceProbe SG365 Designed to hybridize with
cRNA of the human gene NUMA1 365ccccaacact cgcagtggaa cccgccgttc
tccgcgcatt gccaccacca 5036650DNAArtificial SequenceProbe SG366
Designed to hybridize with cRNA of the human gene POU2F2
366ccaactggcc ccagtacaaa gatcaaggct gaagacccca gtggcgattc
5036750DNAArtificial SequenceProbe SG367 Designed to hybridize with
cRNA of the human gene POU2F2 367tcccaagctt ccagcagtct gagcacaaca
gttactacct tatcctcagc 5036850DNAArtificial SequenceProbe SG368
Designed to hybridize with cRNA of the human gene OGGI
368gaccccatcg aatgcctttt ctcttttatc tgttcctcca acaacaacat
5036950DNAArtificial SequenceProbe SG369 Designed to hybridize with
cRNA of the human gene CDKN2B 369gcggatccca acggagtcaa ccgtttcggg
aggcgcgcga tccaggtcat 5037050DNAArtificial SequenceProbe SG370
Designed to hybridize with cRNA of the human gene CDKN2A
370tgaggagcca gcgtctaggg cagcagccgc ttcctagaag accaggtcat
5037150DNAArtificial SequenceProbe SG371 Designed to hybridize with
cRNA of the human gene CDKN2C 371ttagcctgat gcaggcaaac ggggctgggg
gagccacaaa tcttcaataa 5037250DNAArtificial SequenceProbe SG372
Designed to hybridize with cRNA of the human gene CDKN1A
372gaggcccgtg agcgatggaa cttcgacttt gtcaccgaga caccactgga
5037350DNAArtificial SequenceProbe SG373 Designed to hybridize with
cRNA of the human gene CDKN1B 373cctgcaaccg acgattcttc tactcaaaac
aaaagagcca acagaacaga 5037450DNAArtificial SequenceProbe SG374
Designed to hybridize with cRNA of the human gene CDK5R1
374agaacctgaa gaagtcgctg tcgtgcgcca acctgtccac attcgcccag
5037550DNAArtificial SequenceProbe SG375 Designed to hybridize with
cRNA of the human gene TOPORS 375aaccagccca gtaacattgt gtctcttcaa
actgagccat caaggcaatt 5037650DNAArtificial SequenceProbe SG376
Designed to hybridize with cRNA of the human gene P55CDC
376ggatgcccat tcccaggtgt gctccatcct ctggtctccc cattacaagg
5037750DNAArtificial SequenceProbe SG377 Designed to hybridize with
cRNA of the human gene CDKN1C 377cgcctgagaa gtcgtcgggc gatgtccccg
cgccgtgtcc ctctccaagc 5037850DNAArtificial SequenceProbe SG378
Designed to hybridize with cRNA of the human gene TP73
378ctgcatcgag tatttcacct cccaagggtt acagagcatt taccacctgc
5037950DNAArtificial SequenceProbe SGD379 esigned to hybridize with
cRNA of the human gene PAX5 379cccccccgct ggacagggca gctactcagc
accgacgctg acagggatgg 5038050DNAArtificial SequenceProbe SG380
Designed to hybridize with cRNA of the human gene PBX1
380acagtccgca gggcatcagt gctaatggag gttggcagga tgctactacc
5038150DNAArtificial SequenceProbe SG381 Designed to hybridize with
cRNA of the human gene PBX3 381ccaaattccg gttcttctgg ttcttttaac
ctcccaaatt ctggggacat 5038250DNAArtificial SequenceProbe SG382
Designed to hybridize with cRNA of the human gene ENPP1
382aaacatctat gctgtcaaga ccgccgtgtc agtcacccag gggggccaca
5038350DNAArtificial SequenceProbe SG383 Designed to hybridize with
cRNA of the human gene PCA1 383tcactggact cagcttctat caacaaagaa
aagagccagt ttcagacatt 5038450DNAArtificial SequenceProbe SG384
Designed to hybridize with cRNA of the human gene PCNA
384gctcctgaag ccgaaaccag ctagactttc ctccttcccg cctgcctgta
5038550DNAArtificial SequenceProbe SG385 Designed to hybridize with
cRNA of the human gene PDGFRB 385acgactatat catccccctg cctgacccca
aacccgaggt tgctgacgag 5038650DNAArtificial SequenceProbe SG386
Designed to hybridize with cRNA of the human gene PRKCQ
386ggctgtcatt tgccgacaga gcactgatca acagcatgga ccagaatatg
5038750DNAArtificial SequenceProbe SG387 Designed to hybridize with
cRNA of the human gene PLK1 387cctcagcaac ggcagcgtgc agatcaactt
cttccaggat cacaccaagc 5038850DNAArtificial SequenceProbe SG388
Designed to hybridize with cRNA of the human gene PML 388actcaagaac
ctggcccaga cctacctggc gagaaacatg agcgagcgca 5038950DNAArtificial
SequenceProbe SG389 Designed to hybridize with cRNA of the human
gene PRAME 389tttgatgagt gtgggatcac ggatgatcag ctccttgccc
tcctgccttc 5039050DNAArtificial SequenceProbe SG390 Designed to
hybridize with cRNA of the human gene PRKCI 390tctcagttta
ctaatgaacc tgtccagctc actccagatg acgatgacat 5039150DNAArtificial
SequenceProbe SG391 Designed to hybridize with cRNA of the human
gene PTEN 391atattctgac accactgact ctgatccaga gaatgaacct tttgatgaag
5039250DNAArtificial SequenceProbe SG392 Designed to hybridize with
cRNA of the human gene PTGS1 392gtacagctac gagcagttct tgttcaacac
ctccatgttg gtggactatg 5039350DNAArtificial SequenceProbe SG393
Designed to hybridize with cRNA of the human gene PTHLH
393agtgactggg agtgggctag aaggggacca cctgtctgac acctccacaa
5039450DNAArtificial SequenceProbe SG394 Designed to hybridize with
cRNA of the human gene SPI1 394gatctatacc aacgccaaac gcacgagtat
tacccctatc tcagcagtga 5039550DNAArtificial SequenceProbe SG395
Designed to hybridize with cRNA of the human gene PTK2B
395ggagcgtgga tgatctcctg ccttccttgc cgtcatcttc acggacagag
5039650DNAArtificial SequenceProbe SG396 Designed to hybridize with
cRNA of the human gene RAD51 396ggttccttga gcacccggaa acggtcacga
gacccagagg aagaattata 5039750DNAArtificial SequenceProbe SG397
Designed to hybridize with cRNA of the human gene RAG1
397ggcaagctta ggggacccat taggcataga ggactctctg gaaagccaag
5039850DNAArtificial SequenceProbe SG398 Designed to hybridize with
cRNA of the human gene RARA 398cagcttccag ttagtggata tagcacacca
tccccagcca ccattgagac 5039950DNAArtificial SequenceProbe SG399
Designed to hybridize with cRNA of the human gene KRAS2
399gttgatgatg ccttctatac attagttcga gaaattcgaa aacataaaga
5040050DNAArtificial SequenceProbe SG400 Designed to hybridize with
cRNA of the human gene RB1 400aactggcaga aatgacttct actcgaacac
gaatgcaaaa gcagaaaatg 5040150DNAArtificial SequenceProbe SG401
Designed to hybridize with cRNA of the human gene VEGF
401aaatgttcct gcaaaaacac acactcgcgt tgcaaggcga ggcagcttga
5040250DNAArtificial SequenceProbe SG402 Designed to hybridize with
cRNA of the human gene ZYX 402gaagaagttc ggccctgtgg tggccccaaa
gcccaaagtg aatcccttcc 5040350DNAArtificial SequenceProbe SG403
Designed to hybridize with cRNA of the human gene CD28
403cccctatttc ccggaccttc taagcccttt tgggtgctgg tggtggttgg
5040450DNAArtificial SequenceProbe SG404 Designed to hybridize with
cRNA of the human gene CD28 404caaaattgaa gttatgtatc ctcctcctta
cctagacaat gagaagagca 5040550DNAArtificial SequenceProbe SG405
Designed to hybridize with cRNA of the human gene RBBP4
405ttctgtatca gaagacaata tcatgcaagt gtggcaaatg gcagagaaca
5040650DNAArtificial SequenceProbe SG406 Designed to hybridize with
cRNA of the human gene DDX6 406tgtatgtggc agaataccac agcgagcctg
tagaagatga gaaaccttaa 5040750DNAArtificial SequenceProbe SG407
Designed to hybridize with cRNA of the human gene APEX
407gcgccttgat tactttttgt tgtcccactc tctgttacct gcattgtgtg
5040850DNAArtificial SequenceProbe SG408 Designed to hybridize with
cRNA of the human gene DPF2 408cagggcatcc atcttgcctc caatttaccc
ccgtgatgat ggcggcagtg 5040950DNAArtificial SequenceProbe SG409
Designed to hybridize with cRNA of the human gene RGS1
409ctggcttgtg aagactataa gaaaacagag tctgatcttt tgccctgtaa
5041050DNAArtificial SequenceProbe SG410 Designed to hybridize with
cRNA of the human gene HMMR 410tttgccctga agaccccatt aaaagaaggc
aatacaaact gttaccgagc 5041150DNAArtificial SequenceProbe SG411
Designed to hybridize with cRNA of the human gene STAT5B
411tccttgacac cgatggggac ttcgatctgg aggacacaat ggacgtagcg
5041250DNAArtificial SequenceProbe SG412 Designed to hybridize with
cRNA of the human gene BIRC5 412cgctttcctt tctgtcaaga agcagtttga
agaattaacc cttggtgaat 5041350DNAArtificial SequenceProbe SG413
Designed to hybridize with cRNA of the human gene TAL1
413ttccccctat gagatggaga ttactgatgg tccccacacc aaagttgtgc
5041450DNAArtificial SequenceProbe SG414 Designed to hybridize with
cRNA of the human gene NXF1 414tatggtgaag gaaaccgtag gtctggaaga
ggcggttctg gtattcggtc 5041550DNAArtificial SequenceProbe SG415
Designed to hybridize with cRNA of the human gene TCL1A
415ttctggtgga gagaagtgag aataggcagc ccccaaataa aaaatattca
5041650DNAArtificial SequenceProbe SG416 Designed to hybridize with
cRNA of the human gene TRA@ 416attattccag aagacacctt cttccccagc
ccagaaagtt cctgtgatgt 5041750DNAArtificial SequenceProbe SG417
Designed to hybridize with cRNA of the human gene TCR beta
417cagccgtgta tctccgtgcc agcagcttca aaggtgccca ggccggttag
5041850DNAArtificial SequenceProbe SG418 Designed to hybridize with
cRNA of the human gene DNTT 418ctgtatttgg agtggggctg aagacttctg
agaagtggtt caggatgggt 5041950DNAArtificial SequenceProbe SG419
Designed to hybridize with cRNA of the human gene TERT
419attcctgctc aagctgactc gacaccgtgt cacctacgtg ccactcctgg
5042050DNAArtificial SequenceProbe SG420 Designed to hybridize with
cRNA of the human gene ERBB4 420ttgacaaccc tgactactgg aaccacagcc
tgccacctcg gagcaccctt 5042150DNAArtificial SequenceProbe SG421
Designed to hybridize with cRNA of the human gene ERBB2
421cacccagcac cttcaaaggg acacctacgg cagagaaccc agagtacctg
5042250DNAArtificial SequenceProbe SG422 Designed to hybridize with
cRNA of the human gene EGFR 422cccagaaagg cagccaccaa attagcctgg
acaaccctga ctaccagcag 5042350DNAArtificial SequenceProbe SG423
Designed to hybridize with cRNA of the human gene THPO
423cttctaaaca catcctacac ccactcccag aatctgtctc aggaagggta
5042450DNAArtificial SequenceProbe SG424 Designed to hybridize with
cRNA of the human gene TIAM1 424aggaagtcat ttgggttagg cgtgaagact
ttgccccctc caggaaactg 5042550DNAArtificial SequenceProbe SG425
Designed to hybridize with cRNA of the human gene TK1 425ggaagctctt
tgccccacag cagattctgc aatgcagccc tgccaactga 5042650DNAArtificial
SequenceProbe SG426 Designed to hybridize with cRNA of the human
gene TNFRSF1A 426agaagtggga ggacagcgcc cacaagccac agagcctaga
cactgatgac 5042750DNAArtificial SequenceProbe SG427 Designed to
hybridize with cRNA of the human gene TOP2A 427gcctgatcct
gccaaaacca agaatcgccg caaaaggaag ccatccactt 5042850DNAArtificial
SequenceProbe SG428 Designed to hybridize with cRNA of the human
gene FAIM3 428accagcctgc cgccatgatg gaggacagtg attcagatga
ctacatcaat 5042950DNAArtificial SequenceProbe SG429 Designed to
hybridize with cRNA of the human gene PLS3 429gtggcaatct aacagaagat
gacaagcaca ataatgccaa gtatgcagtg 5043050DNAArtificial SequenceProbe
SG430 Designed to hybridize with cRNA of the human gene TRADD
430cgccacctgc ccagactttt ctgttccagg gtcagcctgt agtgaatcgg
5043150DNAArtificial SequenceProbe SG431 Designed to hybridize with
cRNA of the human gene TNFSF10 431gtaacaaatg agcacttgat agacatggac
catgaagcca gttttttcgg 5043250DNAArtificial SequenceProbe SG432
Designed to hybridize with cRNA of the human gene TRAP 1
432aagtttgagg acaggtcccc agccgccgag tgcctatcag agaaggagac
5043350DNAArtificial SequenceProbe SG433 Designed to hybridize with
cRNA of the human gene THBS1 433tagagtggtg atgtatgaag ggaagaaaat
catggctgac tcaggaccca 5043450DNAArtificial SequenceProbe SG434
Designed to hybridize with cRNA of the human gene SUMO1
434atgtgattga agtttatcag gaacaaacgg ggggtcattc aacagtttag
5043550DNAArtificial SequenceProbe SG435 Designed to hybridize with
cRNA of the human gene UVRAG 435gaagaaatca tcgggctgga agcacaggtt
tcgcctcagg tgatcagcta 5043650DNAArtificial SequenceProbe SG436
Designed to hybridize with cRNA of the human gene VPREB1
436ctgtcctgct catgctgttt gtctactgca caggttgtgg tcctcagccg
5043750DNAArtificial SequenceProbe SG437 Designed to hybridize with
cRNA of the human gene WNT16 437tggtgctgct atgtccgttg caggaggtgt
gaaagcatga ctgatgtcca 5043850DNAArtificial SequenceProbe SG438
Designed to hybridize with cRNA of the human gene WT1 438accacagcac
agggtacgag agcgataacc acacaacgcc catcctctgc 5043950DNAArtificial
SequenceProbe SG439 Designed to hybridize with cRNA of the human
gene XRCC3 439gacaccttgt tggagtgtgt gaataagaag gtccccgtac
tgctgtctcg 5044050DNAArtificial SequenceProbe SG440 Designed to
hybridize with cRNA of the human gene CCND3 440ttataccttt
gccatgtacc cgccatccat gatcgccacg ggcagcattg 5044150DNAArtificial
SequenceProbe SG441 Designed to hybridize with cRNA of the human
gene CDK2 441accctttctt ccaggatgtg accaagccag taccccatct tcgactctga
5044250DNAArtificial SequenceProbe SG442 Designed to hybridize with
cRNA of the human gene p14ARF 442aataaaataa ggggaatagg ggagcgggga
cgcgagcagc accagaatcc 5044350DNAArtificial SequenceProbe SG443
Designed to hybridize with cRNA of the human gene HELLS
443gaccgagaaa gagctgttgt ggaagtgaat atccctgtag aatctgaagt
5044450DNAArtificial SequenceProbe SG444 Designed to hybridize with
cRNA of the human gene GATA2 444tttcggcttc ccacccacgc cacccaaaga
agtgtctcct gaccctagca 5044550DNAArtificial SequenceProbe SG445
Designed to hybridize with cRNA of the human gene GATA1
445atccggccca agaagcgcct gattgtcagt aaacgggcag gtactcagtg
5044650DNAArtificial SequenceProbe SG446 Designed to hybridize with
cRNA of the human gene MLLT10 446ttaaattctc aacagctcac accagtacac
aggcaccccc acttcacaca 5044750DNAArtificial SequenceProbe SG447
Designed to hybridize with cRNA of the human gene PICALM
447cggaaatgga accactaaga atgatgtaaa ttggagtcaa ccaggtgaaa
5044850DNAArtificial SequenceProbe SG448 Designed to hybridize with
cRNA of the human gene KIT 448atgtatgaca taatgaagac ttgctgggat
gcagatcccc taaaaagacc 5044950DNAArtificial SequenceProbe SG449
Designed to hybridize with cRNA of the human gene IL3RA
449gcctggagga gtgtctggtg actgaagtac aggtcgtgca gaaaacttga
5045050DNAArtificial SequenceProbe SG450 Designed to hybridize with
cRNA of the human gene CEBPA 450aacgtggaga cgcagcagaa ggtgctggag
ctgaccagtg acaatgaccg 5045150DNAArtificial SequenceProbe SG451
Designed to hybridize with cRNA of the human gene ITGA6
451agatccatgc tcagccatct gataaagaga ggcttacttc tgatgcatag
5045250DNAArtificial SequenceProbe SG452 Designed to hybridize with
cRNA of the human gene CML66 452caggttgcta agcagcaagt agcaagccta
gaaaccaatg atcctatttt 5045350DNAArtificial SequenceProbe SG453
Designed to hybridize with cRNA of the human gene TRAF3
453actggagaga tgaatatcgc ctctggctgc ccagtctttg tggcccaaac
5045450DNAArtificial SequenceProbe SG454 Designed to hybridize with
cRNA of the human gene DAPK1 454ccttttgctg aaggcatcct ctgtgttcaa
aatcaacctg gatggcaatg 5045550DNAArtificial SequenceProbe SG455
Designed to hybridize with cRNA of the human gene MAP3K12
455cttcccggcc tgcaaccccc aaaatggatt ctgcgaggat gacaatgttt
5045650DNAArtificial SequenceProbe SG456 Designed to hybridize with
cRNA of the human gene PRKDC 456ttaggattaa ttgagtggct tgaaaatact
gttaccttga aggaccttct 5045750DNAArtificial SequenceProbe SG457
Designed to hybridize with cRNA of the human gene DNMT3B
457ggcggaagcc catgcaacga tctctcaaat gtgaatccag ccaggaaagg
5045850DNAArtificial SequenceProbe SG458 Designed to hybridize with
cRNA of the human gene GSTP1 458cctcccctga gtacgtgaac ctccccatca
atggcaacgg gaaacagtga 5045950DNAArtificial SequenceProbe SG459
Designed to hybridize with cRNA of the human gene HLA-DRA
459agccctgtgg aactgagaga gcccaacgtc ctcatctgtt tcatcgacaa
5046050DNAArtificial SequenceProbe SG460 Designed to hybridize with
cRNA of the human gene HOXA10 460tcccttcgcc aaattatccc acaacaatgt
catcgtcgga gagccccgcc 5046150DNAArtificial SequenceProbe SG461
Designed to hybridize with cRNA of the human gene IRF8
461ggatatggcc cccttgcgct ccaaactcat tctcgtgcag attgagcagc
5046250DNAArtificial SequenceProbe SG462 Designed to hybridize with
cRNA of the human gene ID2 462aattcccttc tgagttaatg tcaaatgaca
gcaaagcact gtgtggctga 5046350DNAArtificial SequenceProbe SG463
Designed to hybridize with cRNA of the human gene ACTB
463tgatgatatc gccgcgctcg tcgtcgacaa cggctccggc atgtgcaagg
5046450DNAArtificial SequenceProbe SG464 Designed to hybridize with
cRNA of the human gene ACTB 464acgttgctat ccaggctgtg ctatccctgt
acgcctctgg ccgtaccact 5046550DNAArtificial SequenceProbe SG465
Designed to hybridize with cRNA of the human gene GRK4
465atggtgaaac cccgtctcta ctaaaaatac aaaaattagc cgggcgtggt
5046650DNAArtificial SequenceProbe SG466 Designed to hybridize with
cRNA of the human gene GAPD 466tgcttttaac tctggtaaag tggatattgt
tgccatcaat gaccccttca 5046750DNAArtificial SequenceProbe SG467
Designed to hybridize with cRNA of the human gene GAPD
467gtctcctctg acttcaacag cgacacccac tcctccacct ttgacgctgg
5046850DNAArtificial SequenceProbe SG468 Designed to hybridize with
cRNA of the human gene STAT1 468atccaaatat tgacaaagac catgcctttg
gaaagtatta ctccaggcca 5046950DNAArtificial SequenceProbe SG469
Designed to hybridize with cRNA of the human gene 18S rRNA
469ttgactatct agaggaagta aaagtcgtaa caaggtttcc gtaggtgaac
5047050DNAArtificial SequenceProbe SG470 Designed to hybridize with
cRNA of the human gene TFRC 470ccagctttac tggagaactt gaaactgcgt
aaacaaaata acggtgcttt 5047150DNAArtificial SequenceProbe SG471
Designed to hybridize with cRNA of the human gene 28S rRNA
471tctccccttc cttggtgcct tctcggctct tgacacttag ccgctgtctc
5047250DNAArtificial SequenceProbe SG472 Designed to hybridize with
cRNA of the human gene RPL37A 472tcacggtaaa gtccgccatc agaagactga
aggagttgaa agaccagtag 5047350DNAArtificial SequenceProbe SG473
Designed to hybridize with cRNA of the human gene RPL41
473tggaggaaga agcgaatgcg caggctgaag cgcaaaagaa gaaagatgag
5047450DNAArtificial SequenceProbe SG474 Designed to hybridize with
cRNA of the human gene HNRPL 474acccttacac tctgaagttg tgtttctcca
ctgctcagca cgcctcctaa 5047550DNAArtificial SequenceProbe SG475
Designed to hybridize with cRNA of the human gene ILF2
475ctatcttgct tctgaaatat ctacctggga tggagtgata gtaacacctt
5047650DNAArtificial SequenceProbe SG476 Designed to hybridize with
cRNA of the human gene TAGLN2 476gttccctaag aaatccaagg agaatcctcg
gaacttctca gataaccagc 5047750DNAArtificial SequenceProbe SG477
Designed to hybridize with cRNA of the human gene CANP2
477aaggcattag aagaagcagg tttcaagatg ccctgtcaac tccaccaagt
5047850DNAArtificial SequenceProbe SG478 Designed to hybridize with
cRNA of the human gene PSMA5 478accacaagtc tatgactttg aaagaagcca
tcaagtcttc actcatcatc 5047950DNAArtificial SequenceProbe SG479
Designed to hybridize with cRNA of the human gene PMM1
479atccacttct ttgggaacga gactagccct ggtgggaacg actttgagat
5048050DNAArtificial SequenceProbe SG480 Designed to hybridize with
cRNA of the human gene MLF2 480aatacgggtg atggtgcccc caaggtctac
caagagacat cagagatgcg 5048150DNAArtificial SequenceProbe SG481
Designed to hybridize with cRNA of the human gene PPP1CC
481gagacctgta acgcctccaa ggggtatgat cacaaagcaa gcaaagaaat
5048250DNAArtificial SequenceProbe SG482 Designed to hybridize with
cRNA of the human gene CASC3 482atcacaggta tatggaggag tgacctacta
taaccccgcc cagcagcagg 5048350DNAArtificial SequenceProbe SG483
Designed to hybridize with cRNA of the human gene KIAA0864
483tgccttacca tctctgccac ctgtggaatc gctgagagat tgccagaagc
5048450DNAArtificial SequenceProbe SG484 Designed to hybridize with
cRNA of the human gene TXNRD1 484gccattggaa tggacgattc cgtcaagaga
taacaacaaa tgttatgcaa 5048550DNAArtificial SequenceProbe SG485
Designed to hybridize with cRNA of the human gene PSMD7
485tgcacaacct catcaacaac aagattgcca accgggatgc agagaagaaa
5048650DNAArtificial SequenceProbe SG486 Designed to hybridize with
cRNA of the human gene EIF2B2 486caccttccta catctaccgc ctgatgagtg
aactctacca tcctgatgat 5048750DNAArtificial SequenceProbe SG487
Designed to hybridize with cRNA of the human gene HLA-A
487tagaaaagga gggagctact ctcaggctgc aagcagtgac agtgcccagg
5048850DNAArtificial SequenceProbe SG488 Designed to hybridize with
cRNA of the human gene MCM7 488ggcagcttca atcgccccag aaatatacgg
gcatgaagat gtgaagaagg 5048950DNAArtificial SequenceDProbe SG489
esigned to hybridize with cRNA of the human gene TNFRSF25
489ctgacctaca cataccgcca ctgctggcct cacaagcccc tggttactgc
5049050DNAArtificial SequenceProbe SG490 Designed to hybridize with
cRNA of the human gene LGALS3 490agtacaatca tcgggttaaa aaactcaatg
aaatcagcaa actgggaatt 5049150DNAArtificial SequenceProbe SG491
Designed to hybridize with cRNA of the human gene HLA-DPA1
491gaacagatta cagcttccac aagttccatt acctgacctt tgtgccctca
5049250DNAArtificial SequenceProbe SG492 Designed to hybridize with
cRNA of the human gene PLAU 492ctcgtctgtt ccctccaagg ccgcatgact
ttgactggaa ttgtgagctg 5049350DNAArtificial SequenceProbe SG493
Designed to hybridize with cRNA of the human gene COL3A1
493tcgaggattc cctggtaatc caggtgcccc aggttctcca ggccctgctg
5049450DNAArtificial SequenceProbe SG494 Designed to hybridize with
cRNA of the human gene ANK2 494ctcagttcct gaggacatct ttgacacaag
gcccatttgg gatgagtcta 5049550DNAArtificial SequenceProbe SG495
Designed to hybridize with cRNA of the human gene SERPINA9
495gcacctctat tgcagaatta caataacaca ttcaataaaa ctaaaatatg
5049650DNAArtificial SequenceProbe SG496 Designed to hybridize with
cRNA of the human gene NPM3 496ggcaccagat tgttacgatg agcaatgatg
tttctgagga ggagagcgag 5049750DNAArtificial SequenceProbe SG497
Designed to hybridize with cRNA of the human gene CCR6
497gcagaccagt gagaccgcag ataacgacaa tgcgtcgtcc ttcactatgt
5049850DNAArtificial SequenceProbe SG498 Designed to hybridize with
cRNA of the human gene HCK 498ccgagctgcc aacatcttgg tctctgcatc
cctggtgtgt aagattgctg 5049950DNAArtificial SequenceProbe SG499
Designed to hybridize with cRNA of the human gene GNL3
499aggacataca tgaagaattg ccaaaacgga aagaaaggaa gcaggaggag
5050050DNAArtificial SequenceProbe SG500 Designed to hybridize with
cRNA of the human gene GRB2 500ccggcatgtt tccccgcaat tatgtcaccc
ccgtgaaccg gaacgtctaa 5050150DNAArtificial SequenceProbe SG501
Designed to hybridize with cRNA of the human gene BCL2A1
501ggagttcata atgaataaca caggagaatg gataaggcaa aacggaggct
5050250DNAArtificial SequenceProbe SG502 Designed to hybridize with
cRNA of the human gene ELF1 502gtttagaggt ctaatgctat gttttcatat
tacagagtga atttgtattt 5050350DNAArtificial SequenceProbe SG503
Designed to hybridize with cRNA of the human gene CTSB
503tgctctacaa gtcaggagtg taccaacacg tcaccggaga gatgatgggt
5050450DNAArtificial SequenceProbe SG504 Designed to hybridize with
cRNA of the human gene GCET2 504atcctggttc tctctcttcc tccatctgtg
actttgaaca tgctacttgg 5050550DNAArtificial SequenceProbe SG505
Designed to hybridize with cRNA of the human gene FN1 505tcgtgctttg
acccctacac agtttcccat tatgccgttg gagatgagtg 5050650DNAArtificial
SequenceProbe SG506 Designed to hybridize with cRNA of the human
gene PDCD1 506ttcctagcgg aatgggcacc tcatcccccg cccgcagggg
ctcagccgac 5050750DNAArtificial SequenceProbe SG507 Designed to
hybridize with cRNA of the human gene HLA-DRB3 507gttcatctac
ttcaggaatc agaaaggaca ctctggactt cagccaacag 5050850DNAArtificial
SequenceProbe SG508 Designed to hybridize with cRNA of the human
gene HLA-DQA1 508gcagtcagtc acagaagatg tttctgagac cagcttcctc
tccaagagtg 5050950DNAArtificial SequenceProbe SG509 Designed to
hybridize with cRNA of the human gene GCET2 509ggtgaaggct
ccacaaacct gtgacacatg caagctcaag ccattgcatt 5051050DNAArtificial
SequenceProbe SG510 Designed to hybridize with cRNA of the human
gene SERPNINA9 510ggagccccaa ggaatgaaat atggtaaccc agcaacatcc
catgaagcta 5051150DNAArtificial SequenceProbe SG511 Designed to
hybridize with cRNA of the human gene CDKN3 511ctgcacatct
atcatcaaga gattcacaat caagatctgt atcaagataa 5051250DNAArtificial
SequenceProbe SG512 Designed to hybridize with cRNA of the human
gene ELF1 512cttctctcaa gcttcttggc cttcaagtat tctttctcta tcgtcttttg
5051350DNAArtificial SequenceProbe SG513 Designed to hybridize with
cRNA of the human gene CATSD 513gtgccgctga ttcagggcga gtacatgatc
ccctgtgaga aggtgtccac 5051450DNAArtificial SequenceProbe SG514
Designed to hybridize with cRNA of the human gene HSPB1
514atggctacat ctcccggtgc ttcacgcgga aatacacgct gccccccggt
5051550DNAArtificial SequenceProbe SG515 Designed to hybridize with
cRNA of the human gene ACTN1 515cccctacaca accatcacgc ctcaggagat
caatggcaaa tgggaccacg 5051650DNAArtificial SequenceProbe SG516
Designed to hybridize with cRNA of the human gene BMP6
516gaaccccgag tatgtcccca aaccgtgctg tgcgccaact aagctaaatg
5051750DNAArtificial SequenceProbe SG517 Designed to hybridize with
cRNA of the human gene FAM38A 517gtctgtggtc atccccaatc tcttccccaa
gtacatccgt gcccccaacg 5051850DNAArtificial SequenceProbe SG518
Designed to hybridize with cRNA of the human gene CD48
518ttatacttgc caagtcagca attctgtgag cagcaagaat ggcaccgtct
5051950DNAArtificial SequenceProbe SG519 Designed to hybridize with
cRNA of the human gene IL4R 519tcacagtggg agaagcggtc ccgaggccag
gaaccagcca agtgcccaca 5052050DNAArtificial SequenceProbe SG520
Designed to hybridize with cRNA of the human gene DRP2
520ccagtgtgcg aagttctgat gtgactgcca acaccctgct ggcctcttga
5052150DNAArtificial SequenceProbe SG521 Designed to hybridize with
cRNA of the human gene JUNB 521ggaggacaag gtgaagacgc tcaaggccga
gaacgcgggg ctgtcgagta 5052250DNAArtificial SequenceProbe SG522
Designed to hybridize with cRNA of the human gene S100A8
522aattgctaga gaccgagtgt cctcagtata tcaggaaaaa gggtgcagac
5052350DNAArtificial SequenceProbe SG523 Designed to hybridize with
cRNA of the human gene ZNFN1A1 523agttggaggc attcgacttc ctaacggaaa
actaaagtgt gatatctgtg 5052450DNAArtificial SequenceProbe SG524
Designed to hybridize with cRNA of the human gene MERTK
524tcattgcccg atgaactttt gtttgctgac gactcctcag aaggctcaga
5052550DNAArtificial SequenceProbe SG525 Designed to hybridize with
cRNA of the human gene KLF13 525tgcctagtgc tgaggcctct ggggctggaa
agcctcagca gaaaggaggc 5052650DNAArtificial SequenceProbe SG526
Designed to hybridize with cRNA of the human gene CBFB
526aatttcccct gagggaatcg ctttttaagt gatccttaca gtggtgtttt
5052750DNAArtificial SequenceProbe SG527 Designed to hybridize with
cRNA of the human gene CEBPB 527tcctctccga cctcttctcc gacgactacg
ggggcaagaa ctgcaagaag 5052850DNAArtificial SequenceProbe SG528
Designed to hybridize with cRNA of the human gene CEBPD
528cggggcggga gagactcagc aacgacccat acctcagacc cgacggcccg
5052950DNAArtificial SequenceProbe SG529 Designed to hybridize with
cRNA of the human gene TFCP2 529ctgcagttga gggagcagca acaacagcag
cagcaacagc agcagaagca 5053050DNAArtificial SequenceProbe SG530
Designed to hybridize with cRNA of the human gene CREB1
530cgcctgtaat cccagcactt tgggaggcca aggtgggtgg atcacctgtg
5053150DNAArtificial SequenceProbe SG531 Designed to hybridize with
cRNA of the human gene NFIC 531gcggcgatta ctacacttcg cccagctcgc
ccacgagtag cagccgcaac 5053250DNAArtificial SequenceProbe SG532
Designed to hybridize with cRNA of the human gene GABPB2
532tgctccattg tccaattctt cagaaactcc agtagtggcc acagaagaag
5053350DNAArtificial SequenceProbe SG533 Designed to hybridize with
cRNA of the human gene EGR1 533gatggcttga catgtgcaat tgtgagggac
atgctcacct ctagccttaa 5053450DNAArtificial SequenceProbe SG534
Designed to hybridize with cRNA of the human gene KLF1
534gccactaccg gaaacacacg gggcagcgcc ccttccgctg ccagctctgc
5053550DNAArtificial SequenceProbe SG535 Designed to hybridize with
cRNA of the human gene ELF1 535tatggctgac cctgtttcag aagcaggata
gtataaaagc atcagcctaa 5053650DNAArtificial SequenceProbe SG536
Designed to hybridize with cRNA of the human gene ETS1
536ctcgagctgg ccccagactt tgttggggac atcttatggg aacatctaga
5053750DNAArtificial SequenceProbe SG537 Designed to hybridize with
cRNA of the human gene ETS2 537tatttgaaat aagaattcag acatctgagg
ttttatttca tttttcaata 5053850DNAArtificial SequenceProbe SG538
Designed to hybridize with cRNA of the human gene FLI1
538attcgcaagt gctgtgcgct tgtcagacca tcagaccagg gccaaccaat
5053950DNAArtificial SequenceProbe SG539 Designed to hybridize with
cRNA of the human gene GATA3 539gagccctgct cgatgctcac agggccccca
gcgagagtcc ctgcagtccc 5054050DNAArtificial SequenceProbe SG540
Designed to hybridize with cRNA of the human gene CBFA2T1
540tgttggacaa atgtgaagat gcattgtagt ttaaccatat gcccacattt
5054150DNAArtificial SequenceProbe SG541 Designed to hybridize with
cRNA of the human gene HIF1A 541atgcattctt agcaaaattg cctagtatgt
taatttgctc aaaatacaat 5054250DNAArtificial SequenceProbe SG542
Designed to hybridize with cRNA of the human gene TCF1
542cccgagcagc tgagcagggc cggggaactg gccaagctga ggtgcccagg
5054350DNAArtificial SequenceProbe SG543 Designed to hybridize with
cRNA of the human gene HOXD8 543caaatttccc gtttcccggc aggaggtgaa
ggacggggaa acgaaaaagg 5054450DNAArtificial SequenceProbe SG544
Designed to hybridize with cRNA of the human gene HOXD9
544cctcagcttg cagcgaccac ccgatcccag gctgttcgct gaaggaggag
5054550DNAArtificial SequenceProbe SG545 Designed to hybridize with
cRNA of the human gene MAFB 545agcgctccta gggtgagagg cttagccatc
cctgaccctg gcagtgcact 5054650DNAArtificial SequenceProbe SG546
Designed to hybridize with cRNA of the human gene MAFK
546gcggcgggca ggcgggtggg ggcacacccc tcgtacctgt cactgggatg
5054750DNAArtificial SequenceProbe SG547 Designed to hybridize with
cRNA of the human gene EDF1 547ttggccgcca gttccgttct cctcacgggc
cgaacggaac aaggggtcca 5054850DNAArtificial SequenceProbe SG548
Designed to hybridize with cRNA of the human gene ELF4
548ctagatgggg tccaccccca ttcctgctca agcatgggca cctaccacat
5054950DNAArtificial SequenceProbe SG549 Designed to hybridize with
cRNA of the human gene ZNF42 549tccgcgtaca cacgggcgag aaaccctttg
cctgccccga gtgtggccag 5055050DNAArtificial SequenceProbe SG550
Designed to hybridize with cRNA of the human gene NF1 550ggaattgatg
aagaaaccag tgaagaatcc ctcctgactc ccacatctcc 5055150DNAArtificial
SequenceProbe SG551 Designed to hybridize with cRNA of the human
gene NFATC1 551ttctcgtctc acgcagttcg aggaggaccc tagaaagcca
ggagctgtga 5055250DNAArtificial SequenceProbe SG552 Designed to
hybridize with cRNA of the human gene PAX6 552ggtgtgtcag ttccagttca
agttcccgga agtgaacctg atatgtctca 5055350DNAArtificial SequenceProbe
SG553 Designed to hybridize with cRNA of the human gene PAX8
553gcaccacccc aggtcctcct gcagtgcggc atccccttgg cagctgccgt
5055450DNAArtificial SequenceProbe SG554 Designed to hybridize with
cRNA of the human gene PLP 554gccagtgatg gtgggtgggg gctgggcctt
ccccgccacc tccacccctg 5055550DNAArtificial SequenceProbe SG555
Designed to hybridize with cRNA of the human gene PLZF
555gtgctccctc tcactggtgg ggcgtggctt cctcacagag agggacgaca
5055650DNAArtificial SequenceProbe SG556 Designed to hybridize with
cRNA of the human gene RBP4 556gtacaggctg atcgtccaca acggttactg
cgatggcaga tcagaaagaa 5055750DNAArtificial SequenceProbe SG557
Designed to hybridize with cRNA of the human gene RORA
557cagacctgga gcgccacaca ctgcacatct tttggtgatc ggggtcaggc
5055850DNAArtificial SequenceProbe SG558 Designed to hybridize with
cRNA of the human gene SP1 558cctgcttccc cttcctaagt ctgtcatcct
ctggaaggga tgggtggtgc 5055950DNAArtificial SequenceProbe SG559
Designed to hybridize with cRNA of the human gene STAT1
559atatcaatag aaggatgtac atttccaaat tcacaagttg tgtttgatat
5056050DNAArtificial SequenceProbe SG560 Designed to hybridize with
cRNA of the human gene TBP 560tgcagggtgt ggcaccaggt gatgcccttc
tgtaagtgcc caccgcggga 5056150DNAArtificial SequenceProbe SG561
Designed to hybridize with cRNA of the human gene TCF7
561aagggctgcc gggccaggcg cggtggctca cgcctgtaat cccagcactt
5056250DNAArtificial SequenceProbe SG562 Designed to hybridize with
cRNA of the human gene ETV7 562cagccattgc ttgggaaggc tgggaggcct
cccatccagg acactggggg 5056350DNAArtificial SequenceProbe SG563
Designed to hybridize with cRNA of the human gene ZAP70
563cgcggaagga gcagggcaca tacgccctgt ccctcatcta tgggaagacg
5056455DNAArtificial SequenceNegative control 564ggggaaagaa
agatcgatga gaaagaggaa cggggattga caggaatgaa gaagg
5556550DNAArtificial SequenceNegative control 565cgtctcggtg
aactcaagtg aatcaaggga agagaattcc taactgcacg 5056655DNAArtificial
SequenceNegative control 566tcagcttcct ttctcccttt cctccttcct
tccttctcac catcctgtcc ttttt 5556755DNAArtificial SequenceNegative
control 567gaggaaacag gaaagaagag gaaggaagga agacagggaa gaaaagaggg
aggga 5556854DNAArtificial SequenceNegative control 568tctgtgggga
ggggttgttt tggggttgtt tttgtttttt cttgccaggt agat
5456955DNAArtificial SequenceNegative control 569ctctctctct
ctctctctct ctctctgtct ctccccacct ctctcacatc ccttg
5557050DNAArtificial SequenceNegative control 570tgtgtgtgtg
tgtgtgtgtg tgtgtgtgtg tggtgttgtg tgtgtttgtg 5057125DNAArtificial
SequenceNegative control 571gtcgtcaaga tgctaccgtt cagga
2557250DNAArtificial SequencePositive hybridization control
572aggccgtgaa gatatattca tcagctacca tgcgaaagac gatgtccaaa
5057350DNAArtificial SequencePositive hybridization control
573cgagccaggc aaagcggagt aactcagttc gaagtaaggg gaaaatgtcg
5057450DNAArtificial SequenceGives rise to non-specific
hybridization 574gcttttcttc gtttatcatc accatcacca tcatcatcat
catcatcatc 5057550DNAArtificial SequenceNegative control
575gccaggatct caaacccacc aaaccgttcc agaatcatgg accgctttcg
5057650DNAArtificial SequencePositive hybridization control
576gtccaagcga gaagatactt aacaatatca acattaccat taccagcaga
5057750DNAArtificial SequenceNegative control 577atcccgatgc
aaaaggcgga cgacaaggac tacggtctag aagctctgga 5057850DNAArtificial
SequencePositive hybridization control 578ccacatcacc ttcaccattt
ttcttcttcg ttgattctct gtttgtgttt 5057950DNAArtificial SequenceGives
rise to non-specific hybridization 579tcctctgttt tgctcttgcc
ttatccgctg cttctctctc cctctctttc 5058050DNAArtificial
SequenceNegative control 580tgtgacacga cctacaacaa tggctgcaac
ggtggtctca tggactatgc 5058150DNAArtificial SequencePositive
hybridization control 581agaataataa atgaagtgat gatgattgat
gattgatgat tgatgattat 5058250DNAArtificial SequencePositive
hybridization control 582agtgacaagt ttcgctgatt atagtggtta
atgctggtct tatcttcgtc 5058350DNAArtificial SequencePositive
hybridization control 583atgggcggtg cggggttgat gttgacgacg
gtgtggctgc ggttgggtat 5058450DNAArtificial SequenceActs as positive
internal process control spiked control 584cctcaacgcc tacaaaagcc
agtttatccc gtcaaaggat tccgtttcta 5058550DNAArtificial SequenceActs
as positive internal process control spiked control 585cgttatacgg
aagatgatga accgcttcat gccactgaat acgttgaaaa 5058650DNAArtificial
SequenceActs as positive internal process control spiked control
586ctaccaagtg gctaaacgga ccgcagattt gtacggaaaa gaaatgcctc
5058750DNAArtificial SequenceActs as positive internal process
control spiked control 587aacacaagcg gtttccacca tgtccacaag
aaaggggagg taacaccagg 5058850DNAArtificial SequenceActs as positive
internal process control spiked control 588gccagcaaca actcaaccag
caacaaaacc agtttcacag gtgtcaggac 5058950DNAArtificial SequenceActs
as positive internal process control spiked control 589aagcagattc
agtagcagat gccgttcaaa aggtcgattt aagtagaagt 5059050DNAArtificial
SequenceActs as positive internal process control spiked control
590gacttcctga tattgttgat acatgcggaa cagggggaga cggtatttcc
5059170DNAArtificial SequenceAntisense oligonucleotide C2
complementary to SCN2. Biotin residue at 5' 591acgctataaa
catccactac cgacattttc cccttacttt gaactgagtt actccgcttt 60gcctggctcg
7059270DNAArtificial SequenceAntisense oligonucleotide C3
complementary to SCN3.Biotin residue at 5' 592gagcgaaccg gcgtaagttg
tttggacatc gtctttcgca tggtagctga tgaatatatc 60ttcacggcct
7059370DNAArtificial SequenceAntisense oligonucleotide C6
complementary to SCN6. Biotin residue at n 5' 593atcatacgcc
acttcatgtt tctgctggta atggtaatgt tgatattgtt aagtatcttc 60tcgcttggac
7059470DNAArtificial SequenceAntisense oligonucleotide C8
complementary to SCN8. Residue of biotin at 5' 594actgaaaaca
gaacaaacac aaacacaaac agagaatcaa cgaagaagaa aaatggtgaa 60ggtgatgtgg
7059570DNAArtificial SequenceAntisense oligonucleotide C11
complementary to SCN11. Residue of biotin at 5' 595aacattcaag
catgatgatg ataatcatca atcatcaatc atcaatcatc atcacttcat 60ttattattct
7059670DNAArtificial SequenceAntisense oligonucleotide C12
complementary to SCN12. Residue of biotin at 5' 596ttaggattct
aaatagtagc gacgaagata agaccagcat taaccactat aatcagcgaa 60acttgtcact
7059770DNAArtificial SequenceAntisense oligonucleotide C13
complementary to SCN13. Residue of biotin at 5' 597tctgaaggct
tgcttgatcc atacccaacc gcagccacac cgtcgtcaac atcaaccccg 60caccgcccat
7059824DNAArtificial SequencePrimer PSMB4_Forward of Gene PSMB4
598ttctgggaga tggacacagc tata 2459921DNAArtificial SequencePrimer
PSMB4_Reverse of Gene PSMB4 599ccacaaaggg ttcatcttcg a
2160021DNAArtificial SequencePrimer CD23A_Forward of Gene CD23A
600tgccctgaaa agtggatcaa t 2160121DNAArtificial SequencePrimer
CD23A_Reverse of Gene CD23A 601ccatgtcgtc acaggcatac c
2160221DNAArtificial SequencePrimer LCP1_Forward of Gene LCP1
602ccaggtaccc ttctcgcttt t 2160320DNAArtificial SequencePrimer
LCP1_Reverse of Gene LCP1 603ctcctggccc tcatcttgaa
2060424DNAArtificial SequencePrimer ABCC5_Forward of Gene ABCC5
604ccctcaaagt ctgcaacttt aagc 2460521DNAArtificial SequencePrimer
ABCC5_Reverse of Gene ABCC5 605acacaccaaa ccacacagca a
2160621DNAArtificial SequencePrimer POU2F2_Forward of Gene POU2F2
606gaggaccagc atcgagacaa a 2160720DNAArtificial SequencePrimer
POU2F2_Reverse of Gene POU2F2 607aaccagacgc ggatcacttc 20
* * * * *
References